Variant report

Variant	rs12002094
Chromosome Location	chr9:117190749-117190750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117187233..117189197-chr9:117190405..117194407,3	K562	blood:
2	chr9:117189063..117191201-chr9:117373805..117375386,2	K562	blood:

Variant related genes	Relation type
ENSG00000095397	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10081697	0.84[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10739411	0.84[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10739412	0.84[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs10739413	0.84[CHB][hapmap]
rs10739414	0.84[CHB][hapmap]
rs10759694	0.90[CEU][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs10759698	0.90[CEU][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs10759699	0.90[CEU][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10817598	0.86[EUR][1000 genomes]
rs10817602	0.86[CEU][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs10817607	0.90[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10817609	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10982193	0.89[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs10982201	0.88[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs10982203	0.87[EUR][1000 genomes]
rs10982212	0.84[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10982213	0.90[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1324635	0.84[CHB][hapmap]
rs2274158	0.90[CEU][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs2274161	0.84[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2274162	0.90[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2274163	0.83[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs3748174	0.84[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3748175	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4978584	0.90[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4979375	0.90[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs4979378	0.90[CEU][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4979379	0.90[CEU][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs4979382	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4979383	0.90[CEU][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4979385	0.84[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs4979386	0.90[CEU][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4979388	0.94[ASN][1000 genomes]
rs7038862	0.90[CEU][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs7043417	0.86[EUR][1000 genomes]
rs731421	0.90[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs766835	0.88[EUR][1000 genomes]
rs7849013	0.90[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7861409	0.84[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs7864759	0.90[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7875262	0.90[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7875632	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	nsv466533	chr9:116930100-117248479	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
5	nsv615233	chr9:116930100-117248479	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
6	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
17	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv615235	chr9:116958144-117367061	ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
19	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
20	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
21	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
22	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
23	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
24	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
25	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
26	nsv1047704	chr9:116978041-117399362	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
27	nsv540205	chr9:116978041-117399362	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
28	nsv530950	chr9:117009156-117399361	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
29	nsv916139	chr9:117009169-117399454	Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
30	nsv1047822	chr9:117010663-117211517	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
31	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
32	nsv1050256	chr9:117106276-117247033	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
33	nsv540206	chr9:117106276-117247033	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
34	nsv831693	chr9:117116450-117281895	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12002094	C9orf80	cis	parietal	SCAN
rs12002094	GNAI3	trans	parietal	SCAN
rs12002094	SUSD1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117160800-117197000	Weak transcription	Gastric	stomach
2	chr9:117161200-117199200	Weak transcription	Right Atrium	heart
3	chr9:117175400-117196000	Weak transcription	HepG2	liver
4	chr9:117180000-117193600	Weak transcription	Brain Angular Gyrus	brain
5	chr9:117180800-117192800	Weak transcription	Lung	lung
6	chr9:117181600-117196200	Weak transcription	Pancreas	Pancrea
7	chr9:117185800-117197000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr9:117186400-117197200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:117186800-117193200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:117187000-117213800	Weak transcription	Thymus	Thymus
11	chr9:117187200-117192000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:117187400-117197000	Weak transcription	Brain Anterior Caudate	brain
13	chr9:117188200-117192000	Weak transcription	Brain Substantia Nigra	brain
14	chr9:117188600-117197200	Weak transcription	Ovary	ovary
15	chr9:117188600-117197800	Weak transcription	Fetal Stomach	stomach
16	chr9:117189000-117192800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:117189000-117196200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr9:117189000-117215200	Weak transcription	Fetal Intestine Small	intestine
19	chr9:117189600-117191000	Enhancers	Brain Hippocampus Middle	brain
20	chr9:117189600-117191200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:117189800-117192200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:117190200-117190800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:117190200-117193000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr9:117190200-117196000	Weak transcription	Spleen	Spleen
25	chr9:117190200-117197400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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