Variant report

Variant	rs9843295
Chromosome Location	chr3:93790542-93790543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr3:93790515-93791077	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:93790383-93791121	GM12878	blood:	n/a	n/a
3	STAT5A	chr3:93790520-93791097	GM12878	blood:	n/a	chr3:93790955-93790963
4	POLR2A	chr3:93790481-93791159	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:93779019..93784541-chr3:93784932..93791200,12	K562	blood:
2	chr3:93722699..93725451-chr3:93787826..93790801,2	MCF-7	breast:
3	chr3:93779162..93784721-chr3:93784932..93791200,9	K562	blood:
4	chr3:93781324..93783964-chr3:93790114..93791924,2	MCF-7	breast:

Variant related genes	Relation type
NSUN3	TF binding region
ENSG00000178700	Chromatin interaction
ENSG00000178694	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12488200	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs4414894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs4857173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4857343	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs5013930	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6771653	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6773487	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6786905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6803590	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs7650230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs9821535	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9848659	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1795060	chr3:93602038-93848525	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
8	esv1791740	chr3:93602927-93849247	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
9	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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 target site	19 gene(s)	inside rSNPs	n/a
10	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv967185	chr3:93771419-93794318	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	n/a
14	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9843295	TMX4	trans	cerebellum	SCAN
rs9843295	ARL6	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93782400-93804400	Weak transcription	Spleen	Spleen
2	chr3:93782800-93792400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:93782800-93795200	Weak transcription	HSMMtube	muscle
4	chr3:93782800-93795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:93782800-93799200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:93782800-93799600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:93782800-93813400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:93782800-93848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:93782800-93849400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:93783000-93790600	Weak transcription	Esophagus	oesophagus
11	chr3:93783000-93790600	Weak transcription	Gastric	stomach
12	chr3:93783000-93790600	Weak transcription	Lung	lung
13	chr3:93783000-93790600	Weak transcription	Pancreas	Pancrea
14	chr3:93783000-93795000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:93783000-93795000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:93783000-93795200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:93783000-93795200	Weak transcription	NH-A	brain
18	chr3:93783000-93803000	Weak transcription	Psoas Muscle	Psoas
19	chr3:93783000-93810600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:93783000-93813800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:93783000-93813800	Weak transcription	Right Ventricle	heart
22	chr3:93783200-93824600	Weak transcription	NHEK	skin
23	chr3:93783200-93851600	Weak transcription	HMEC	breast
24	chr3:93783400-93790600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:93783400-93791800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:93783400-93795200	Weak transcription	HSMM	muscle
27	chr3:93783400-93813800	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:93783400-93833000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:93783600-93799000	Weak transcription	Colonic Mucosa	Colon
30	chr3:93783600-93837800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:93784000-93792000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:93784400-93790600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:93784400-93790600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:93784400-93796800	Weak transcription	K562	blood
35	chr3:93784400-93802000	Weak transcription	Small Intestine	intestine
36	chr3:93784600-93799000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:93784600-93814000	Weak transcription	A549	lung
38	chr3:93784600-93817400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:93784800-93820200	Weak transcription	Hela-S3	cervix
40	chr3:93785000-93790600	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:93785200-93795000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:93785600-93834400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:93786200-93790600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:93786200-93790600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:93786200-93795000	Weak transcription	Fetal Thymus	thymus
46	chr3:93786200-93798800	Weak transcription	HepG2	liver
47	chr3:93786200-93804200	Weak transcription	Thymus	Thymus
48	chr3:93786200-93834600	Weak transcription	Brain Substantia Nigra	brain
49	chr3:93786400-93790600	Weak transcription	Brain Germinal Matrix	brain
50	chr3:93786400-93830800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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