Variant report

Variant	rs6433760
Chromosome Location	chr2:180017152-180017153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10170520	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10174774	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10186198	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10188759	0.84[TSI][hapmap]
rs10192426	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10205390	0.94[JPT][hapmap]
rs10205999	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10209887	0.84[TSI][hapmap]
rs10439299	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10930858	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1158872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11884516	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11894870	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11898291	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12622075	0.84[TSI][hapmap]
rs12997314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13026497	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13382185	0.84[TSI][hapmap]
rs13383965	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13391602	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13418701	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1374378	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1374379	0.85[EUR][1000 genomes]
rs1446674	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs1907421	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1979053	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2008989	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2008999	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2289992	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2847	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs340331	0.82[GIH][hapmap]
rs4585064	0.91[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6433757	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433761	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433764	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433769	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6707081	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6734121	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6736098	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6742739	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6743405	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6756326	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7562730	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7579536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7585600	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7608882	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9288022	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3060	chr2:179990791-180035511	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6433760	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs6433760	SESTD1	cis	parietal	SCAN
rs6433760	SESTD1	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
4	chr2:179980000-180038800	Weak transcription	HMEC	breast
5	chr2:179980000-180056800	Weak transcription	HSMM	muscle
6	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
7	chr2:179986600-180030400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
9	chr2:179996200-180047600	Weak transcription	NH-A	brain
10	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
11	chr2:180002400-180030200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:180003200-180039800	Weak transcription	Brain Germinal Matrix	brain
13	chr2:180004800-180019200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:180004800-180046000	Weak transcription	Spleen	Spleen
15	chr2:180005000-180028800	Weak transcription	Hela-S3	cervix
16	chr2:180005600-180040200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:180005600-180044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:180005600-180044400	Weak transcription	Esophagus	oesophagus
19	chr2:180005800-180018200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:180005800-180030200	Weak transcription	Thymus	Thymus
21	chr2:180005800-180043200	Weak transcription	Fetal Brain Male	brain
22	chr2:180005800-180053600	Weak transcription	Primary T cells from cord blood	blood
23	chr2:180006000-180030600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:180006000-180044600	Weak transcription	Pancreas	Pancrea
25	chr2:180006200-180031400	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:180006200-180031400	Weak transcription	Fetal Brain Female	brain
27	chr2:180006400-180030200	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:180006600-180042000	Weak transcription	Brain Substantia Nigra	brain
29	chr2:180006600-180051000	Weak transcription	HUVEC	blood vessel
30	chr2:180006800-180031600	Weak transcription	Brain Anterior Caudate	brain
31	chr2:180006800-180054600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:180007200-180028600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:180007400-180035200	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:180007400-180035600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:180007400-180042200	Weak transcription	Brain Angular Gyrus	brain
36	chr2:180007400-180043000	Weak transcription	Aorta	Aorta
37	chr2:180007600-180030400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:180007600-180031000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:180007600-180031200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:180008400-180030600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:180008400-180042200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:180008600-180028400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:180008600-180029400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr2:180008600-180037600	Weak transcription	Fetal Thymus	thymus
45	chr2:180008600-180038400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:180008600-180048400	Weak transcription	Small Intestine	intestine
47	chr2:180009000-180026000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:180011200-180029000	Weak transcription	Dnd41	blood
49	chr2:180011800-180039400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:180012000-180023000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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