Variant report

Variant	rs10209887
Chromosome Location	chr2:180104766-180104767
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	chr2:180099965..180101717-chr2:180103234..180105570,2	K562	blood:
2	chr2:180099014..180101971-chr2:180103448..180105283,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10164707	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10164814	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs10174774	0.86[TSI][hapmap]
rs10176829	0.82[AMR][1000 genomes]
rs10177122	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10177402	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10181291	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10182477	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10185803	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10188759	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10194420	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10194534	0.92[EUR][1000 genomes]
rs10196366	0.88[ASN][1000 genomes]
rs10204985	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10209183	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10439300	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs10930859	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11898291	0.84[TSI][hapmap]
rs12105846	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12617002	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12621023	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12621115	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12623243	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12693179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12693181	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12693183	0.84[ASN][1000 genomes]
rs12987285	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12997314	0.84[TSI][hapmap]
rs13020645	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13382185	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13384403	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13392996	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13396340	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13414296	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13417919	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13418701	0.84[TSI][hapmap]
rs1374378	0.84[TSI][hapmap]
rs1446674	0.82[TSI][hapmap]
rs17454311	0.95[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap]
rs2007593	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2166534	0.85[YRI][hapmap]
rs2289992	0.84[TSI][hapmap]
rs28838656	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4585064	0.82[TSI][hapmap]
rs4894082	0.82[YRI][hapmap]
rs57098667	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433760	0.84[TSI][hapmap]
rs6433764	0.84[TSI][hapmap]
rs6433770	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67043078	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6707081	0.84[TSI][hapmap]
rs6731614	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6743405	0.84[TSI][hapmap]
rs6743412	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6759983	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]
rs7569887	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7585600	0.84[TSI][hapmap]
rs7601366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7608745	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7608882	0.84[TSI][hapmap]
rs9288025	0.83[CEU][hapmap]
rs9288026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs10209887	SESTD1	cis	multi-tissue	Pritchard
rs10209887	SESTD1	cis	cerebellum	SCAN
rs10209887	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs10209887	SESTD1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180089600-180115200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
3	chr2:180092800-180112400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:180093000-180107800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:180098000-180105200	Weak transcription	Fetal Thymus	thymus
6	chr2:180098600-180118600	Weak transcription	Pancreas	Pancrea
7	chr2:180100800-180104800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:180100800-180105000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:180100800-180105200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:180101200-180105200	Weak transcription	Aorta	Aorta
11	chr2:180101200-180112200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr2:180101800-180105000	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr2:180101800-180105600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:180101800-180107000	Enhancers	Brain Substantia Nigra	brain
15	chr2:180102000-180105000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:180102000-180105200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:180102000-180105400	Enhancers	Adipose Nuclei	Adipose
18	chr2:180102000-180105800	Enhancers	Brain Cingulate Gyrus	brain
19	chr2:180102200-180105000	Enhancers	HMEC	breast
20	chr2:180102200-180105800	Enhancers	HUVEC	blood vessel
21	chr2:180102400-180105600	Enhancers	Colon Smooth Muscle	Colon
22	chr2:180102400-180106200	Enhancers	Brain Hippocampus Middle	brain
23	chr2:180102600-180105000	Enhancers	Primary T cells from cord blood	blood
24	chr2:180102600-180105200	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:180102800-180104800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:180102800-180104800	Enhancers	Fetal Intestine Large	intestine
27	chr2:180102800-180104800	Enhancers	Fetal Intestine Small	intestine
28	chr2:180102800-180105200	Weak transcription	HSMMtube	muscle
29	chr2:180102800-180105400	Weak transcription	Left Ventricle	heart
30	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
31	chr2:180103000-180105800	Enhancers	Hela-S3	cervix
32	chr2:180103000-180112200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:180103200-180104800	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr2:180103200-180105200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:180103200-180105200	Enhancers	A549	lung
36	chr2:180103200-180105200	Enhancers	NHEK	skin
37	chr2:180103200-180106200	Enhancers	Dnd41	blood
38	chr2:180103200-180116000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:180103400-180105000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:180103400-180105400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr2:180103400-180105400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr2:180103600-180104800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr2:180103600-180105000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:180103600-180105000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr2:180103600-180105000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr2:180103600-180105200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:180103600-180105600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr2:180103600-180105600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr2:180103600-180105800	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr2:180103600-180106200	Enhancers	GM12878-XiMat	blood

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