Variant report

Variant	rs3931416
Chromosome Location	chr3:136260576-136260577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10513016	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs16843978	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs16843991	1.00[CHB][hapmap]
rs16844056	0.81[EUR][1000 genomes]
rs17266364	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs17365351	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs17466223	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs34962604	0.82[AFR][1000 genomes]
rs35375192	1.00[CHB][hapmap];0.89[YRI][hapmap]
rs35644083	1.00[CHB][hapmap];0.85[LWK][hapmap];0.81[AFR][1000 genomes]
rs3932048	0.85[YRI][hapmap]
rs4336059	1.00[CHB][hapmap];0.85[LWK][hapmap]
rs55763637	0.88[EUR][1000 genomes]
rs55848312	0.86[EUR][1000 genomes]
rs56083120	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56218376	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57681357	0.88[EUR][1000 genomes]
rs58636237	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58641485	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616231	0.81[EUR][1000 genomes]
rs59696368	0.81[EUR][1000 genomes]
rs60014495	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60270684	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439642	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs66470158	0.86[EUR][1000 genomes]
rs66471262	0.81[EUR][1000 genomes]
rs66494666	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66739346	0.82[EUR][1000 genomes]
rs66902780	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66973954	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67082054	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67230667	0.86[EUR][1000 genomes]
rs67236827	0.81[EUR][1000 genomes]
rs67281610	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67303976	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67305360	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67621498	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765239	1.00[CHB][hapmap];0.87[LWK][hapmap]
rs67663578	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773495	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773604	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs67794070	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67888773	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67902591	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800969	1.00[CHB][hapmap]
rs6804194	0.84[ASW][hapmap];1.00[CHB][hapmap];0.87[LWK][hapmap];0.89[YRI][hapmap]
rs72975363	0.81[EUR][1000 genomes]
rs73224201	0.84[EUR][1000 genomes]
rs73226130	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228025	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228037	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228040	0.86[EUR][1000 genomes]
rs7612160	0.82[YRI][hapmap]
rs7623824	1.00[CHB][hapmap];0.87[LWK][hapmap]
rs7636806	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644471	1.00[CHB][hapmap];0.85[LWK][hapmap]
rs7646563	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7646723	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7650075	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs923001	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9820513	1.00[CHB][hapmap];0.87[LWK][hapmap]
rs9839574	0.87[LWK][hapmap]
rs9858457	0.85[AFR][1000 genomes]
rs9869957	1.00[CHB][hapmap]

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	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3931416	VCAN	trans	cerebellum	SCAN
rs3931416	TMEM22	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
4	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:136220600-136266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:136222400-136266200	Weak transcription	HSMM	muscle
10	chr3:136232000-136263600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:136246600-136286200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
14	chr3:136247400-136270600	Weak transcription	Fetal Thymus	thymus
15	chr3:136247800-136261600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:136251600-136264400	Weak transcription	Fetal Lung	lung
19	chr3:136251600-136266000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:136251600-136270400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:136251600-136284400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:136251600-136284400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:136251600-136289400	Weak transcription	Adipose Nuclei	Adipose
24	chr3:136251600-136322400	Weak transcription	Liver	Liver
25	chr3:136251800-136262200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:136251800-136266400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:136251800-136284800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:136252000-136270000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:136252600-136262400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:136252600-136264600	Weak transcription	Thymus	Thymus
31	chr3:136252600-136266200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:136252600-136284800	Weak transcription	Left Ventricle	heart
33	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:136252800-136266000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:136252800-136305600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:136252800-136314800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:136253000-136262400	Weak transcription	Primary B cells from cord blood	blood
38	chr3:136253600-136264600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:136254400-136265000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:136255200-136294000	Weak transcription	Primary T cells from cord blood	blood
41	chr3:136255400-136261600	Weak transcription	HUVEC	blood vessel
42	chr3:136255800-136291600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:136256600-136263400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:136256800-136263000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:136256800-136266200	Weak transcription	NHDF-Ad	bronchial
46	chr3:136257600-136267800	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:136257600-136270000	Weak transcription	Fetal Stomach	stomach
48	chr3:136257600-136282800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:136258000-136269800	Weak transcription	Fetal Intestine Small	intestine
50	chr3:136258200-136275400	Weak transcription	Fetal Intestine Large	intestine

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