Variant report

Variant	rs3960984
Chromosome Location	chr3:178879730-178879731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178876883..178879796-chr3:178884449..178887188,2	MCF-7	breast:
2	chr3:178872506..178874182-chr3:178879392..178881985,2	K562	blood:
3	chr3:178876264..178878992-chr3:178879301..178882016,3	K562	blood:
4	chr3:178873426..178875261-chr3:178876713..178879813,4	K562	blood:

Variant related genes	Relation type
ENSG00000201957	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1059691	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10936992	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10936994	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11706842	1.00[CHB][hapmap]
rs11708869	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11919383	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11922631	1.00[CHB][hapmap]
rs11924547	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12488074	0.94[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1568205	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1850504	0.82[CHB][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1970901	0.94[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[LWK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3729674	0.87[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3729676	0.94[ASW][hapmap];0.85[CEU][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3729694	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3975510	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3975513	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3976507	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4080957	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4855093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4855095	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[LWK][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55685804	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56023503	0.94[ASN][1000 genomes]
rs61796482	0.86[EUR][1000 genomes]
rs61796483	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62408837	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6443619	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6443624	0.94[ASW][hapmap];0.82[CHB][hapmap];0.81[LWK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6443625	0.85[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6443626	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6443628	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6443629	1.00[CHB][hapmap]
rs67562832	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67609137	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6767284	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6769154	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[LWK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6769162	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6769508	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6770267	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6777203	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6782557	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6786049	1.00[CHB][hapmap]
rs6786114	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6791153	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67920954	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6794252	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6798817	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6799756	1.00[CHB][hapmap]
rs6803219	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6806917	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6810246	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73051974	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7372645	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7614305	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7614418	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7615076	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7621329	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7621436	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7623154	0.87[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7627273	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7628855	1.00[CHB][hapmap]
rs7635669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7636454	0.81[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7638323	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7641889	0.82[CHB][hapmap]
rs7641983	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7644648	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7646409	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7648857	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7650809	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7651265	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs938752	1.00[CHB][hapmap]
rs9813190	1.00[CHB][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9819762	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9829903	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9831234	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9833438	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9838411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9839519	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9841051	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9844270	1.00[CHB][hapmap]
rs9844482	0.83[ASW][hapmap];1.00[CHB][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs9862294	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9866361	1.00[ASW][hapmap];0.82[CHB][hapmap];0.91[LWK][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9881887	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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 target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
5	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1003540	chr3:178875803-178886293	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1010571	chr3:178876965-178888153	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv822351	chr3:178878517-178883804	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3960984	KCNMB3	cis	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178867600-178882400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:178867600-178883400	Weak transcription	Stomach Mucosa	stomach
3	chr3:178867800-178900200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:178868000-178892400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:178868600-178881400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:178868600-178893000	Weak transcription	Aorta	Aorta
7	chr3:178869200-178898000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:178869400-178887200	Weak transcription	Fetal Brain Male	brain
9	chr3:178869800-178883400	Weak transcription	Liver	Liver
10	chr3:178870000-178880600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:178870800-178896400	Weak transcription	K562	blood
12	chr3:178872400-178883200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:178874000-178880400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr3:178874400-178880200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:178874400-178880600	Weak transcription	HSMM	muscle
16	chr3:178874600-178883000	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:178874800-178883400	Weak transcription	Fetal Kidney	kidney
18	chr3:178874800-178888600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:178875400-178880400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr3:178876800-178884200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:178877000-178883400	Weak transcription	Fetal Heart	heart
22	chr3:178877200-178880400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:178877400-178897800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:178879000-178880200	Weak transcription	Pancreas	Pancrea
25	chr3:178879000-178882400	Weak transcription	Ovary	ovary
26	chr3:178879000-178883200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:178879000-178883200	Weak transcription	Psoas Muscle	Psoas
28	chr3:178879000-178885600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:178879200-178880200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:178879200-178880800	Weak transcription	Primary B cells from cord blood	blood
31	chr3:178879200-178881800	Weak transcription	Primary T cells from cord blood	blood
32	chr3:178879200-178882800	Weak transcription	Adipose Nuclei	Adipose
33	chr3:178879200-178883800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:178879200-178891800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:178879400-178881000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:178879400-178882200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:178879400-178882800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:178879400-178892000	Weak transcription	Lung	lung
39	chr3:178879400-178896400	Weak transcription	Right Atrium	heart
40	chr3:178879600-178881200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:178879600-178883400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:178879600-178896400	Weak transcription	Left Ventricle	heart

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