Variant report

Variant	rs6443629
Chromosome Location	chr3:178967580-178967581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 132 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1059691	0.98[ASN][1000 genomes]
rs10936992	0.93[ASN][1000 genomes]
rs10936994	0.83[ASN][1000 genomes]
rs11706842	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs11708869	0.93[ASN][1000 genomes]
rs1183319	0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs11918324	0.90[ASN][1000 genomes]
rs11918587	0.93[ASN][1000 genomes]
rs11919383	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11922631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11924545	0.83[ASN][1000 genomes]
rs11924547	0.93[ASN][1000 genomes]
rs11924600	0.83[ASN][1000 genomes]
rs11925655	0.93[ASN][1000 genomes]
rs12488074	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1568205	0.95[ASN][1000 genomes]
rs17849071	0.90[ASN][1000 genomes]
rs1850504	0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs1970901	0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[ASN][1000 genomes]
rs1976765	0.93[ASN][1000 genomes]
rs2865082	0.90[ASN][1000 genomes]
rs3729674	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3729676	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3729682	0.90[ASN][1000 genomes]
rs3729694	0.90[ASN][1000 genomes]
rs3960984	1.00[CHB][hapmap]
rs3975510	0.83[ASN][1000 genomes]
rs3975513	0.95[ASN][1000 genomes]
rs3976507	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4080957	0.98[ASN][1000 genomes]
rs4855093	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs4855095	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs55685804	0.90[ASN][1000 genomes]
rs55933053	0.93[ASN][1000 genomes]
rs55961756	0.90[ASN][1000 genomes]
rs56095736	0.98[ASN][1000 genomes]
rs56143971	0.90[ASN][1000 genomes]
rs56372555	0.93[ASN][1000 genomes]
rs56378415	0.88[ASN][1000 genomes]
rs59340081	0.93[ASN][1000 genomes]
rs59408989	0.97[ASN][1000 genomes]
rs59922883	0.93[ASN][1000 genomes]
rs61796482	0.90[ASN][1000 genomes]
rs61796483	0.83[ASN][1000 genomes]
rs62408837	0.90[ASN][1000 genomes]
rs6443619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6443624	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6443625	0.95[ASN][1000 genomes]
rs6443626	0.93[ASN][1000 genomes]
rs6443627	0.93[ASN][1000 genomes]
rs6443628	0.98[ASN][1000 genomes]
rs67562832	0.97[ASN][1000 genomes]
rs67609137	0.93[ASN][1000 genomes]
rs6765953	0.90[ASN][1000 genomes]
rs6767284	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6769154	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6769162	0.98[ASN][1000 genomes]
rs6769508	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6770267	0.93[ASN][1000 genomes]
rs6771313	0.98[ASN][1000 genomes]
rs6774158	0.90[ASN][1000 genomes]
rs6777203	0.90[ASN][1000 genomes]
rs6782557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6786049	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6786114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6791153	0.90[ASN][1000 genomes]
rs67920954	0.90[ASN][1000 genomes]
rs6792189	0.93[ASN][1000 genomes]
rs6794252	0.93[ASN][1000 genomes]
rs6797304	0.93[ASN][1000 genomes]
rs6798817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6799756	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs6803076	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6803219	0.95[ASN][1000 genomes]
rs6806555	0.93[ASN][1000 genomes]
rs6806917	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6810246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs73051974	0.93[ASN][1000 genomes]
rs73187264	0.90[ASN][1000 genomes]
rs73187276	0.90[ASN][1000 genomes]
rs7372645	0.98[ASN][1000 genomes]
rs7612533	0.93[ASN][1000 genomes]
rs7614305	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7614418	0.90[ASN][1000 genomes]
rs7615076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7621329	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7621436	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7623154	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs7624090	0.90[ASN][1000 genomes]
rs7627273	0.93[ASN][1000 genomes]
rs7628855	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs7635669	1.00[CHB][hapmap]
rs7636454	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs7638323	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs7638649	0.93[ASN][1000 genomes]
rs7641889	0.82[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs7641983	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7644648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7645550	0.86[CHD][hapmap]
rs7646409	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7648857	0.93[ASN][1000 genomes]
rs7650809	0.90[ASN][1000 genomes]
rs7651265	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs938752	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs9631497	0.88[ASN][1000 genomes]
rs9813190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9817020	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9819762	0.90[ASN][1000 genomes]
rs9829903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9831234	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9833438	0.98[ASN][1000 genomes]
rs9838411	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs9839519	0.93[ASN][1000 genomes]
rs9841051	0.95[ASN][1000 genomes]
rs9844270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9844482	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9850621	0.93[ASN][1000 genomes]
rs9862294	0.93[ASN][1000 genomes]
rs9866361	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9877812	0.93[ASN][1000 genomes]
rs9881887	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	nsv878039	chr3:178933363-178968568	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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 target site	37 gene(s)	inside rSNPs	diseases
8	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	esv1800747	chr3:178962897-178977074	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv1010137	chr3:178962897-179050787	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6443629	MCF2L2	cis	parietal	SCAN
rs6443629	FAM131A	cis	parietal	SCAN
rs6443629	KCNMB3	cis	multi-tissue	Pritchard
rs6443629	CLCN2	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178912400-178978600	Weak transcription	Right Ventricle	heart
2	chr3:178913800-178969000	Weak transcription	Small Intestine	intestine
3	chr3:178914800-178972800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:178920200-178968400	Weak transcription	Spleen	Spleen
5	chr3:178925800-178968200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:178925800-178968600	Weak transcription	Pancreas	Pancrea
7	chr3:178932200-178974000	Weak transcription	Lung	lung
8	chr3:178941800-178972600	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:178945800-178978400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:178948400-178967600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:178948800-178978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:178949000-178968200	Weak transcription	Fetal Stomach	stomach
13	chr3:178949000-178970800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:178949000-178978200	Weak transcription	NHLF	lung
15	chr3:178949000-178978600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:178949000-178978600	Weak transcription	Ovary	ovary
17	chr3:178949000-178978800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:178949200-178967600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:178949200-178968600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:178949200-178968600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:178949200-178978400	Weak transcription	Brain Anterior Caudate	brain
22	chr3:178949200-178978600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:178949200-178978600	Weak transcription	Osteobl	bone
24	chr3:178949800-178969000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:178952000-178968200	Weak transcription	Fetal Brain Female	brain
26	chr3:178952000-178978400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:178952200-178968400	Weak transcription	Fetal Lung	lung
28	chr3:178952200-178970400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:178952200-178973000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:178952400-178967800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:178952400-178967800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:178952400-178971200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:178952400-178971400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:178952400-178978600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:178952600-178967600	Weak transcription	Fetal Kidney	kidney
36	chr3:178952600-178967800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:178952600-178967800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:178952600-178976600	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:178954600-178970800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:178954600-178972400	Weak transcription	Fetal Intestine Small	intestine
41	chr3:178955000-178973800	Weak transcription	HSMMtube	muscle
42	chr3:178955200-178974400	Weak transcription	GM12878-XiMat	blood
43	chr3:178955400-178970600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:178956200-178977000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:178959800-178978800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:178963000-178968800	Weak transcription	Primary B cells from cord blood	blood
47	chr3:178963200-178968000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:178963200-178970000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr3:178963200-178970600	Weak transcription	Placenta	Placenta
50	chr3:178963200-178971000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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