Variant report

Variant	rs7601200
Chromosome Location	chr2:113089267-113089268
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	chr2:113032266..113035570-chr2:113088065..113092560,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10167748	0.96[ASN][1000 genomes]
rs10175234	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10177573	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10183121	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs10191002	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10203614	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10203843	0.96[ASN][1000 genomes]
rs10205038	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10205897	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10211300	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10439391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10864903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11123132	0.94[CHB][hapmap];1.00[YRI][hapmap]
rs11123135	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123136	0.93[ASN][1000 genomes]
rs11674953	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11691431	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs11896500	0.94[ASN][1000 genomes]
rs11903741	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11904424	0.91[ASN][1000 genomes]
rs12464478	0.85[ASN][1000 genomes]
rs12464895	1.00[YRI][hapmap]
rs12711738	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12711739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13387611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34471791	0.86[ASN][1000 genomes]
rs4258804	0.96[ASN][1000 genomes]
rs4299347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4332934	0.96[ASN][1000 genomes]
rs4352239	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392265	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4399734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4419238	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4430968	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4446076	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4450606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4450607	0.95[ASN][1000 genomes]
rs4456711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4507112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4522611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4525706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4539797	0.96[ASN][1000 genomes]
rs4542853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4578863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622729	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4630773	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849058	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58337061	0.96[ASN][1000 genomes]
rs62160223	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6542045	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6542051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6542052	0.91[ASN][1000 genomes]
rs6542053	1.00[ASN][1000 genomes]
rs6542054	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706874	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs6708164	0.97[ASN][1000 genomes]
rs6716010	0.85[EUR][1000 genomes]
rs6725933	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6726412	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6733138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6744364	0.98[ASN][1000 genomes]
rs6751146	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6758110	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6761599	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71414636	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7557281	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7557862	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7564052	0.96[ASN][1000 genomes]
rs7569894	1.00[ASN][1000 genomes]
rs7571435	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7579561	0.98[ASN][1000 genomes]
rs7591439	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7598168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7599041	0.96[ASN][1000 genomes]
rs7600338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7601888	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8179708	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv874869	chr2:113021811-113089267	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv874874	chr2:113027569-113089267	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv874876	chr2:113051291-113089267	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7601200	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs7601200	RGPD8	cis	lung	GTEx
rs7601200	RGPD8	cis	Muscle Skeletal	GTEx
rs7601200	FBLN7	cis	parietal	SCAN
rs7601200	RGPD8	cis	Artery Tibial	GTEx
rs7601200	LOC653596	cis	multi-tissue	Pritchard
rs7601200	RGPD8	cis	Nerve Tibial	GTEx
rs7601200	POLR1B	cis	parietal	SCAN
rs7601200	TMEM87B	cis	parietal	SCAN
rs7601200	POLR1B	cis	cerebellum	SCAN
rs7601200	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113034400-113097000	Weak transcription	Psoas Muscle	Psoas
2	chr2:113050600-113090600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:113057000-113099400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:113058200-113090600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:113059200-113096800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:113059600-113090000	Weak transcription	Colonic Mucosa	Colon
7	chr2:113060000-113090600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:113060400-113090600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:113062200-113094400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:113062400-113090600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:113068200-113101400	Weak transcription	NHDF-Ad	bronchial
12	chr2:113069000-113097000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:113070000-113093600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:113075400-113094400	Weak transcription	NHLF	lung
15	chr2:113079800-113093200	Weak transcription	HSMM	muscle
16	chr2:113081400-113091200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:113081800-113092200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:113082200-113091800	Weak transcription	GM12878-XiMat	blood
19	chr2:113082200-113094200	Weak transcription	Small Intestine	intestine
20	chr2:113082200-113097000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:113082200-113097000	Weak transcription	Gastric	stomach
22	chr2:113082800-113091000	Weak transcription	HSMMtube	muscle
23	chr2:113083000-113089400	Weak transcription	Brain Germinal Matrix	brain
24	chr2:113083000-113097000	Weak transcription	Pancreas	Pancrea
25	chr2:113083400-113096400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:113084000-113090000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:113084400-113089800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:113084800-113091600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:113085800-113092800	Weak transcription	Fetal Intestine Small	intestine
30	chr2:113085800-113103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:113086000-113089400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:113086000-113090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:113086000-113091400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:113086000-113092600	Weak transcription	Liver	Liver
35	chr2:113086000-113093000	Weak transcription	Fetal Brain Male	brain
36	chr2:113086000-113097000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:113086800-113090000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:113087000-113089400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:113087000-113089800	Strong transcription	Primary B cells from cord blood	blood
40	chr2:113087000-113089800	Strong transcription	Brain Hippocampus Middle	brain
41	chr2:113087000-113090000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr2:113087200-113089800	Strong transcription	Adipose Nuclei	Adipose
43	chr2:113087400-113089600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr2:113087400-113089800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr2:113087400-113089800	Strong transcription	Brain Angular Gyrus	brain
46	chr2:113087600-113090000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:113088000-113089600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr2:113088000-113089800	Strong transcription	Primary T cells from cord blood	blood
49	chr2:113088000-113089800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:113088000-113089800	Strong transcription	Fetal Lung	lung

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