Variant report

Variant	rs1039912
Chromosome Location	chr8:8648229-8648230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:8647143..8649997-chr8:8748170..8750908,2	MCF-7	breast:
2	chr8:8648185..8650191-chr8:8651639..8653893,2	MCF-7	breast:
3	chr8:8641971..8645218-chr8:8645421..8648443,3	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10087633	0.86[EUR][1000 genomes]
rs10087742	0.85[EUR][1000 genomes]
rs10090152	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10092600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10092720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10093872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10094270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10098636	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10099808	0.84[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs10100066	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10103163	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10103282	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10105690	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10105920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10109886	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10110711	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10112989	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10113326	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1039910	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1039911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10503392	0.81[ASN][1000 genomes]
rs11249892	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11774744	0.81[ASN][1000 genomes]
rs11774860	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs11775821	0.81[ASN][1000 genomes]
rs11775888	0.81[ASN][1000 genomes]
rs11776513	0.81[ASN][1000 genomes]
rs11776546	0.81[ASN][1000 genomes]
rs11776845	0.85[ASN][1000 genomes]
rs11778970	0.81[ASN][1000 genomes]
rs11779561	0.85[EUR][1000 genomes]
rs11779565	0.83[EUR][1000 genomes]
rs11781430	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11781542	0.81[ASN][1000 genomes]
rs11783112	0.81[ASN][1000 genomes]
rs11784958	0.81[ASN][1000 genomes]
rs11785741	0.85[EUR][1000 genomes]
rs11906	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11987146	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11987904	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11987924	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11997731	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11997763	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12155530	0.81[ASN][1000 genomes]
rs17154702	0.81[ASN][1000 genomes]
rs2427	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs28402110	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28521727	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28583936	0.85[ASN][1000 genomes]
rs34473848	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34732488	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35457364	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3827807	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3827808	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs3827811	0.84[CEU][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs4840356	0.81[ASN][1000 genomes]
rs4841030	0.81[ASN][1000 genomes]
rs4841031	0.81[ASN][1000 genomes]
rs55816468	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55971558	0.81[ASN][1000 genomes]
rs56007835	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57301822	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66564323	0.85[ASN][1000 genomes]
rs66618176	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67000451	0.85[ASN][1000 genomes]
rs67653033	0.85[ASN][1000 genomes]
rs67766414	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6985207	0.92[ASN][1000 genomes]
rs7002397	1.00[CHB][hapmap]
rs73198272	0.81[ASN][1000 genomes]
rs73198279	0.81[ASN][1000 genomes]
rs73198286	0.81[ASN][1000 genomes]
rs73198287	0.81[ASN][1000 genomes]
rs73198288	0.81[ASN][1000 genomes]
rs73198290	0.81[ASN][1000 genomes]
rs73201840	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7813355	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7820324	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7837843	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7838012	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs964771	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1022511	chr8:8493992-8737132	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv539457	chr8:8493992-8737132	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
11	esv1795023	chr8:8583943-8655580	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	esv1825234	chr8:8583943-8655580	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	esv1824870	chr8:8583943-8699382	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv610189	chr8:8590437-8664940	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	nsv831228	chr8:8608387-8790790	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	5 gene(s)	inside rSNPs	diseases
16	nsv1018828	chr8:8609880-8790660	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv1022331	chr8:8610035-8787981	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats 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	4 gene(s)	inside rSNPs	diseases
18	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1039912	PPP1R3B	cis	cerebellum	SCAN
rs1039912	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8631000-8648400	Weak transcription	Fetal Stomach	stomach
2	chr8:8631200-8652400	Weak transcription	Ovary	ovary
3	chr8:8637600-8648800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:8637600-8653400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr8:8637600-8679800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:8637800-8651000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr8:8638200-8651000	Weak transcription	Fetal Intestine Large	intestine
8	chr8:8640200-8655600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:8640400-8649000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr8:8640600-8648600	Weak transcription	A549	lung
11	chr8:8640600-8652000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr8:8640600-8653200	Weak transcription	Gastric	stomach
13	chr8:8640600-8654800	Weak transcription	Colonic Mucosa	Colon
14	chr8:8640800-8648800	Weak transcription	Small Intestine	intestine
15	chr8:8640800-8652400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr8:8641200-8648800	Weak transcription	Stomach Mucosa	stomach
17	chr8:8641200-8652400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr8:8641400-8651000	Weak transcription	Aorta	Aorta
19	chr8:8641600-8652200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr8:8641600-8653000	Weak transcription	Liver	Liver
21	chr8:8641800-8649400	Enhancers	Fetal Lung	lung
22	chr8:8642400-8648400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:8642800-8648400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr8:8642800-8660000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr8:8643600-8648600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr8:8643600-8652200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr8:8644200-8655600	Weak transcription	Fetal Brain Male	brain
28	chr8:8644600-8650800	Weak transcription	Fetal Brain Female	brain
29	chr8:8644800-8652000	Weak transcription	NHEK	skin
30	chr8:8645000-8649200	Enhancers	Fetal Heart	heart
31	chr8:8645000-8655000	Weak transcription	Brain Angular Gyrus	brain
32	chr8:8645200-8649600	Enhancers	Spleen	Spleen
33	chr8:8645400-8648800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr8:8645800-8649400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr8:8646000-8648600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr8:8646200-8649400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr8:8646200-8649400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr8:8646200-8649400	Enhancers	Primary hematopoietic stem cells	blood
39	chr8:8646200-8649400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr8:8646400-8649200	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr8:8646400-8649400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr8:8646400-8649400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr8:8646400-8649400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr8:8646600-8649200	Enhancers	Colon Smooth Muscle	Colon
45	chr8:8646600-8651800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr8:8646600-8654600	Weak transcription	Brain Hippocampus Middle	brain
47	chr8:8646600-8654800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr8:8646600-8655000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr8:8646600-8655000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr8:8646600-8658000	Weak transcription	Pancreas	Pancrea

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