Variant report

Variant	rs9831321
Chromosome Location	chr3:136142592-136142593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12330800	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12635723	0.92[YRI][hapmap]
rs1279425	0.89[YRI][hapmap]
rs16843991	0.95[CEU][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2305265	1.00[CHD][hapmap]
rs28396702	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34165586	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34523567	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34962604	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35058853	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35375192	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35644083	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3732519	1.00[CHD][hapmap]
rs3755636	0.89[YRI][hapmap]
rs3821444	1.00[CHD][hapmap]
rs3932048	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs4678428	0.89[YRI][hapmap]
rs5026242	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs548288	0.89[YRI][hapmap]
rs55797013	0.83[EUR][1000 genomes]
rs56040643	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56251259	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs576771	0.89[YRI][hapmap]
rs6439638	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6439642	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67214626	0.80[EUR][1000 genomes]
rs6766450	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6776841	1.00[CEU][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6782151	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6783337	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6789761	0.81[EUR][1000 genomes]
rs6799368	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6804194	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs699165	0.82[YRI][hapmap]
rs7612160	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs7615706	0.85[AMR][1000 genomes]
rs7620314	0.81[CEU][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap]
rs7621017	0.81[AMR][1000 genomes]
rs7622833	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7644471	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7648591	0.85[AMR][1000 genomes]
rs9809184	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9811261	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9811490	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9812319	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9812513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9819496	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9826146	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs9833162	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9843348	0.81[EUR][1000 genomes]
rs9843801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs9850383	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9853387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9854084	0.82[YRI][hapmap]
rs9858457	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9860801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9866535	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9868120	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9872326	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9831321	RNF184	cis	multi-tissue	Pritchard
rs9831321	ZBTB38	cis	cerebellum	SCAN
rs9831321	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
4	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:136085800-136174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:136086200-136174800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:136110800-136174200	Weak transcription	Esophagus	oesophagus
8	chr3:136112200-136174200	Weak transcription	Osteobl	bone
9	chr3:136113000-136174200	Weak transcription	Aorta	Aorta
10	chr3:136114800-136160400	Weak transcription	Fetal Kidney	kidney
11	chr3:136115400-136174200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:136116200-136173400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:136116600-136174400	Weak transcription	Hela-S3	cervix
14	chr3:136118200-136170400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:136123000-136157000	Weak transcription	Colonic Mucosa	Colon
16	chr3:136124600-136174000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:136129800-136174200	Weak transcription	HSMMtube	muscle
18	chr3:136131000-136160200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:136131400-136160400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:136131400-136175400	Weak transcription	HMEC	breast
21	chr3:136132000-136145400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:136133000-136160400	Weak transcription	Spleen	Spleen
23	chr3:136133200-136173800	Weak transcription	Fetal Heart	heart
24	chr3:136133600-136173400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:136135200-136173400	Weak transcription	NHEK	skin
26	chr3:136137800-136156200	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:136138200-136173600	Weak transcription	Brain Angular Gyrus	brain
28	chr3:136138400-136167000	Weak transcription	HSMM	muscle
29	chr3:136138800-136150600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:136138800-136171400	Weak transcription	HepG2	liver
31	chr3:136138800-136174200	Weak transcription	Brain Anterior Caudate	brain
32	chr3:136139400-136144000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:136139600-136159600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:136139800-136143200	Weak transcription	Primary B cells from cord blood	blood
35	chr3:136139800-136145200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:136139800-136145800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:136139800-136146800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:136139800-136150200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:136139800-136150600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:136139800-136159600	Weak transcription	Ovary	ovary
41	chr3:136139800-136160000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:136139800-136160400	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:136139800-136160400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:136139800-136161000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:136139800-136162600	Weak transcription	Fetal Brain Male	brain
46	chr3:136139800-136163200	Weak transcription	Psoas Muscle	Psoas
47	chr3:136139800-136175400	Weak transcription	Small Intestine	intestine
48	chr3:136139800-136175800	Weak transcription	Right Ventricle	heart
49	chr3:136140000-136142600	Weak transcription	Fetal Intestine Small	intestine
50	chr3:136140000-136143400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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