Variant report

Variant	rs10177122
Chromosome Location	chr2:180126625-180126626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180115733..180117570-chr2:180124952..180126888,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10164707	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10164814	0.80[ASN][1000 genomes]
rs10177402	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181291	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10181464	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10182477	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185803	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194420	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194534	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10196366	0.80[ASN][1000 genomes]
rs10204985	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209183	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209887	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10439300	0.85[AFR][1000 genomes]
rs10930859	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12105846	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12617002	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12621023	0.92[EUR][1000 genomes]
rs12621115	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12622075	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623243	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693179	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12693181	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693183	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12987285	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13020645	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13382185	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13384403	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392996	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13396340	0.85[EUR][1000 genomes]
rs13414296	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13417919	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007593	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28838656	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57098667	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433770	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67043078	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731614	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6743412	0.88[ASN][1000 genomes]
rs6759983	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7569887	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7601366	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7608745	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9288026	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10177122	SESTD1	cis	multi-tissue	Pritchard
rs10177122	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

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	chr2:180112600-180126800	Weak transcription	Hela-S3	cervix
4	chr2:180115400-180127600	Weak transcription	NHLF	lung
5	chr2:180118800-180127600	Weak transcription	HSMM	muscle
6	chr2:180118800-180128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:180119400-180128200	Weak transcription	Pancreas	Pancrea
8	chr2:180120000-180127400	Weak transcription	Brain Angular Gyrus	brain
9	chr2:180120200-180127200	Weak transcription	Fetal Kidney	kidney
10	chr2:180120200-180127600	Weak transcription	Fetal Stomach	stomach
11	chr2:180120400-180126800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:180122600-180127400	Enhancers	Adipose Nuclei	Adipose
13	chr2:180123600-180126800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:180123800-180127600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:180123800-180127800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:180123800-180127800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:180123800-180128000	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:180124000-180127400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:180124400-180127000	Enhancers	HMEC	breast
20	chr2:180124400-180127600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:180124600-180127200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:180124800-180127400	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr2:180125200-180126800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:180125200-180127000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:180125200-180127000	Flanking Active TSS	HepG2	liver
26	chr2:180125400-180127600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:180125400-180127600	Weak transcription	Aorta	Aorta
28	chr2:180125400-180127600	Weak transcription	Right Atrium	heart
29	chr2:180125400-180128000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:180125400-180128200	Weak transcription	Left Ventricle	heart
31	chr2:180125400-180128200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:180125600-180126800	Weak transcription	Primary B cells from cord blood	blood
33	chr2:180126000-180126800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:180126000-180127400	Enhancers	HUVEC	blood vessel
35	chr2:180126200-180126800	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:180126200-180127200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr2:180126200-180127600	Active TSS	GM12878-XiMat	blood
38	chr2:180126200-180127800	Weak transcription	Stomach Mucosa	stomach
39	chr2:180126400-180127000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:180126400-180127000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr2:180126400-180127200	Enhancers	Small Intestine	intestine
42	chr2:180126400-180127400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:180126400-180127400	Weak transcription	NHEK	skin
44	chr2:180126400-180127600	Enhancers	Dnd41	blood
45	chr2:180126400-180128600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:180126400-180130200	Active TSS	Stomach Smooth Muscle	stomach
47	chr2:180126600-180126800	Weak transcription	Fetal Brain Female	brain
48	chr2:180126600-180127000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr2:180126600-180127200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:180126600-180127400	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links