Variant report

Variant	rs1877631
Chromosome Location	chr17:17030003-17030004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:17029933-17030078	MCF-7	breast:	n/a	n/a
2	CTCF	chr17:17029860-17030010	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17023341..17025938-chr17:17027098..17030092,2	K562	blood:
2	chr17:17028360..17030286-chr17:17031836..17034332,2	MCF-7	breast:

Variant related genes	Relation type
MPRIP	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10852843	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs10852845	0.84[ASN][1000 genomes]
rs11078366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11078370	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs11078371	0.88[MEX][hapmap]
rs11078373	0.88[MEX][hapmap]
rs11078375	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1110504	0.95[ASN][1000 genomes]
rs11651460	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs11652079	0.95[ASN][1000 genomes]
rs11652936	0.82[ASN][1000 genomes]
rs11654247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11654562	0.90[CHB][hapmap]
rs11658084	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap]
rs11658904	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12450213	0.84[ASN][1000 genomes]
rs12450467	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12451054	0.82[ASN][1000 genomes]
rs12452802	0.98[ASN][1000 genomes]
rs12601325	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12602867	1.00[ASN][1000 genomes]
rs16961288	1.00[CHB][hapmap]
rs16961412	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[ASN][1000 genomes]
rs3744132	0.88[MEX][hapmap]
rs3744133	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs3744140	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs4073940	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs4074611	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4264448	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4275916	0.82[ASN][1000 genomes]
rs4606773	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs4621033	0.82[ASN][1000 genomes]
rs4985695	0.82[ASN][1000 genomes]
rs4985697	0.82[ASN][1000 genomes]
rs4985698	0.84[ASN][1000 genomes]
rs4985712	0.84[AMR][1000 genomes]
rs4985714	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[MEX][hapmap]
rs4985715	1.00[CHB][hapmap]
rs4985719	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4985723	0.81[ASN][1000 genomes]
rs4985727	0.82[ASN][1000 genomes]
rs4985739	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs4985744	0.93[ASN][1000 genomes]
rs4985747	0.95[ASN][1000 genomes]
rs55751545	0.98[ASN][1000 genomes]
rs57812549	0.98[ASN][1000 genomes]
rs58472573	0.82[ASN][1000 genomes]
rs61018209	0.93[ASN][1000 genomes]
rs7207187	1.00[CHB][hapmap]
rs7210339	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs7217970	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs7223686	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs73979061	0.82[ASN][1000 genomes]
rs73979081	0.82[ASN][1000 genomes]
rs73979082	0.82[ASN][1000 genomes]
rs73979083	0.82[ASN][1000 genomes]
rs8064991	1.00[ASN][1000 genomes]
rs8067563	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs8073851	0.87[CEU][hapmap]
rs8075751	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes]
rs9910011	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907728	chr17:17013189-17095487	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv984510	chr17:17015688-17048858	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv524958	chr17:17029718-17060805	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1877631	TOM1L2	cis	cerebellum	SCAN
rs1877631	C3orf51	trans	cerebellum	SCAN
rs1877631	MPRIP	cis	lymphoblastoid	seeQTL
rs1877631	M-RIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17006200-17033000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr17:17010000-17032000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:17012000-17035200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr17:17015400-17035200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:17019800-17031200	Weak transcription	Hela-S3	cervix
6	chr17:17023000-17030200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr17:17023200-17034200	Weak transcription	NH-A	brain
8	chr17:17023600-17030600	Weak transcription	Osteobl	bone
9	chr17:17024200-17043200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr17:17024400-17030200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr17:17024400-17030200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr17:17024400-17030200	Weak transcription	HMEC	breast
13	chr17:17024400-17032800	Weak transcription	HUVEC	blood vessel
14	chr17:17024400-17039800	Weak transcription	Small Intestine	intestine
15	chr17:17024600-17036000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr17:17024600-17045600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr17:17024800-17030200	Weak transcription	Liver	Liver
18	chr17:17024800-17030200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr17:17024800-17030600	Weak transcription	HepG2	liver
20	chr17:17024800-17034200	Weak transcription	Fetal Kidney	kidney
21	chr17:17025000-17030200	Weak transcription	Fetal Lung	lung
22	chr17:17025000-17030200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr17:17025000-17031400	Weak transcription	Ovary	ovary
24	chr17:17025000-17031400	Weak transcription	Stomach Mucosa	stomach
25	chr17:17025200-17030200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr17:17026000-17030400	Enhancers	Left Ventricle	heart
27	chr17:17026400-17034200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:17026600-17030200	Weak transcription	Colon Smooth Muscle	Colon
29	chr17:17026600-17030200	Weak transcription	Pancreas	Pancrea
30	chr17:17027200-17032600	Enhancers	Psoas Muscle	Psoas
31	chr17:17027400-17030200	Enhancers	Thymus	Thymus
32	chr17:17027400-17030400	Enhancers	Fetal Thymus	thymus
33	chr17:17027400-17031800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:17027400-17032000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr17:17027400-17032200	Enhancers	Right Atrium	heart
36	chr17:17027400-17042400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr17:17027400-17043000	Strong transcription	NHEK	skin
38	chr17:17027400-17043400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr17:17027600-17030800	Enhancers	Brain Angular Gyrus	brain
40	chr17:17027600-17033400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr17:17027800-17030400	Enhancers	Fetal Brain Male	brain
42	chr17:17027800-17031000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr17:17027800-17032200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr17:17028000-17032000	Enhancers	Fetal Heart	heart
45	chr17:17028000-17038200	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr17:17028200-17030200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr17:17028200-17030200	Enhancers	Brain Germinal Matrix	brain
48	chr17:17028200-17030400	Enhancers	Brain Cingulate Gyrus	brain
49	chr17:17028200-17030400	Enhancers	Brain Hippocampus Middle	brain
50	chr17:17028200-17032400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links