Variant report

Variant	rs6759983
Chromosome Location	chr2:180122829-180122830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180120526..180124742-chr2:180127021..180129947,5	K562	blood:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10164707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10164814	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs10177122	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10177402	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10181291	0.89[ASN][1000 genomes]
rs10181464	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10182477	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10185803	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10188759	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap]
rs10194420	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10194534	0.81[AMR][1000 genomes]
rs10196366	0.80[ASN][1000 genomes]
rs10204985	0.97[ASN][1000 genomes]
rs10209183	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10209887	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10439300	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10930859	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12105846	0.93[ASN][1000 genomes]
rs12617002	1.00[ASW][hapmap];0.83[CEU][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621023	0.89[CEU][hapmap]
rs12621115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12622075	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12623243	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12693179	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12693181	0.89[ASN][1000 genomes]
rs12693183	0.86[ASN][1000 genomes]
rs12987285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13020645	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13382185	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.80[ASN][1000 genomes]
rs13384403	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13392996	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13414296	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13417919	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17454311	0.84[CEU][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap]
rs2007593	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2166534	0.85[YRI][hapmap]
rs28838656	0.80[ASN][1000 genomes]
rs4894082	0.82[YRI][hapmap]
rs57098667	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6433770	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs67043078	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6731614	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7569887	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7601366	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs7608745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9288025	0.94[CEU][hapmap]
rs9288026	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[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	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6759983	SESTD1	cis	multi-tissue	Pritchard
rs6759983	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs6759983	SESTD1	cis	parietal	SCAN
rs6759983	SESTD1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
2	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
3	chr2:180110200-180124200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:180112400-180126200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:180112600-180125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:180112600-180126800	Weak transcription	Hela-S3	cervix
7	chr2:180115400-180127600	Weak transcription	NHLF	lung
8	chr2:180116200-180124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:180116800-180124400	Enhancers	HepG2	liver
10	chr2:180117400-180126200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:180117800-180124400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:180117800-180126400	Weak transcription	Small Intestine	intestine
13	chr2:180118000-180125200	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:180118200-180124800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:180118600-180126200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:180118800-180127600	Weak transcription	HSMM	muscle
17	chr2:180118800-180128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:180119200-180124400	Weak transcription	Primary B cells from cord blood	blood
19	chr2:180119400-180123400	Weak transcription	Brain Substantia Nigra	brain
20	chr2:180119400-180128200	Weak transcription	Pancreas	Pancrea
21	chr2:180119600-180126200	Weak transcription	Brain Anterior Caudate	brain
22	chr2:180120000-180127400	Weak transcription	Brain Angular Gyrus	brain
23	chr2:180120200-180127200	Weak transcription	Fetal Kidney	kidney
24	chr2:180120200-180127600	Weak transcription	Fetal Stomach	stomach
25	chr2:180120400-180125000	Weak transcription	Right Atrium	heart
26	chr2:180120400-180126800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:180121200-180124400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:180121400-180123200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:180122400-180123800	Enhancers	Brain Cingulate Gyrus	brain
30	chr2:180122600-180127400	Enhancers	Adipose Nuclei	Adipose
31	chr2:180122800-180123800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:180122800-180123800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr2:180122800-180124000	Enhancers	Brain Hippocampus Middle	brain

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