Variant report

Variant	rs6768743
Chromosome Location	chr3:136205007-136205008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs12695645	1.00[ASN][1000 genomes]
rs12695649	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066401	1.00[ASN][1000 genomes]
rs13071220	1.00[CEU][hapmap];0.82[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13072038	1.00[ASN][1000 genomes]
rs13092193	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096466	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100192	1.00[ASN][1000 genomes]
rs13316214	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321721	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13326151	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433688	1.00[ASN][1000 genomes]
rs13434116	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1604793	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17200216	1.00[CEU][hapmap]
rs17298525	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364492	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28390205	1.00[ASN][1000 genomes]
rs28472992	1.00[ASN][1000 genomes]
rs28634226	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28641809	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28718456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28750366	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28811905	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28877020	1.00[ASN][1000 genomes]
rs34031772	1.00[ASN][1000 genomes]
rs34135127	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34168675	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34282798	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34428695	1.00[ASN][1000 genomes]
rs34757183	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34804893	0.93[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs34913797	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34969907	1.00[ASN][1000 genomes]
rs35326900	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375192	0.81[GIH][hapmap]
rs35428413	1.00[ASN][1000 genomes]
rs35522825	1.00[ASN][1000 genomes]
rs35899944	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4038586	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66890203	1.00[ASN][1000 genomes]
rs67145204	1.00[ASN][1000 genomes]
rs67382287	1.00[ASN][1000 genomes]
rs6765239	0.81[GIH][hapmap]
rs6767889	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6771002	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773949	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774964	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775314	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67949818	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806123	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71336069	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73230043	1.00[ASN][1000 genomes]
rs7612425	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809269	1.00[ASN][1000 genomes]
rs9810789	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812579	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813115	1.00[ASN][1000 genomes]
rs9813691	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818056	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818536	1.00[ASN][1000 genomes]
rs9820717	0.93[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs9823373	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828088	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832813	0.83[GIH][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap]
rs9837158	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9839137	0.87[AMR][1000 genomes]
rs9841529	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844666	1.00[ASN][1000 genomes]
rs9847427	0.93[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs9857833	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857966	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866840	1.00[ASN][1000 genomes]
rs9869630	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870825	1.00[ASN][1000 genomes]
rs9872178	1.00[ASN][1000 genomes]
rs9875770	1.00[ASN][1000 genomes]
rs9878078	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880211	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs9881831	1.00[ASN][1000 genomes]
rs9883189	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];1.00[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	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	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6768743	PPP2R3A	cis	parietal	SCAN
rs6768743	NCK1	cis	cerebellum	SCAN
rs6768743	ERICH1	trans	parietal	SCAN
rs6768743	RNF184	cis	multi-tissue	Pritchard
rs6768743	PPP2R3A	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:136176600-136222800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:136176600-136224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:136176600-136224400	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:136176600-136231800	Weak transcription	Psoas Muscle	Psoas
7	chr3:136176600-136240000	Weak transcription	HMEC	breast
8	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:136176800-136205800	Weak transcription	Small Intestine	intestine
10	chr3:136176800-136228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
12	chr3:136177200-136236400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:136178000-136212000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:136178400-136208200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:136178600-136220200	Weak transcription	Fetal Brain Male	brain
16	chr3:136179800-136212000	Weak transcription	Fetal Heart	heart
17	chr3:136181200-136205400	Weak transcription	Fetal Kidney	kidney
18	chr3:136181400-136211600	Weak transcription	A549	lung
19	chr3:136183800-136212000	Weak transcription	Lung	lung
20	chr3:136191000-136220000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:136191400-136209400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:136192200-136205400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:136192200-136212600	Weak transcription	Pancreas	Pancrea
25	chr3:136192200-136225600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:136192600-136206000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:136193800-136217200	Weak transcription	HepG2	liver
29	chr3:136193800-136231400	Weak transcription	NHLF	lung
30	chr3:136193800-136239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:136194600-136212000	Weak transcription	Esophagus	oesophagus
32	chr3:136195000-136210600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:136195000-136220400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:136195000-136223000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:136195200-136209800	Weak transcription	NHDF-Ad	bronchial
36	chr3:136195200-136210800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:136195200-136210800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:136195200-136211400	Weak transcription	HSMM	muscle
39	chr3:136195200-136212200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:136195200-136231000	Weak transcription	Osteobl	bone
41	chr3:136195400-136205200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:136195400-136205400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:136195400-136205600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:136195400-136205600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr3:136195400-136205800	Weak transcription	Aorta	Aorta
46	chr3:136195400-136205800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:136195400-136205800	Weak transcription	Left Ventricle	heart
48	chr3:136195400-136206000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:136195400-136209800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:136195400-136209800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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