Variant report

Variant	rs965636
Chromosome Location	chr2:86413450-86413451
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	chr2:86411907..86414408-chr2:86415972..86419181,3	K562	blood:
2	chr2:86413150..86415828-chr2:86422831..86424544,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132305	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1010239	0.81[CEU][hapmap]
rs10173155	1.00[CHB][hapmap]
rs1050301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11127016	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11127019	1.00[YRI][hapmap]
rs11127024	1.00[YRI][hapmap]
rs1131071	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11676515	1.00[YRI][hapmap]
rs11685551	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11689971	1.00[YRI][hapmap]
rs11900161	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs12988844	0.81[MKK][hapmap]
rs13005014	1.00[YRI][hapmap]
rs13024436	1.00[YRI][hapmap]
rs1559514	1.00[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs17438451	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs17438687	0.81[MKK][hapmap]
rs17584697	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17618119	1.00[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17738058	1.00[YRI][hapmap]
rs1863050	0.96[MKK][hapmap]
rs1863056	1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs1863057	1.00[YRI][hapmap]
rs1863060	1.00[YRI][hapmap]
rs1863061	1.00[YRI][hapmap]
rs2042502	1.00[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs2059352	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2081322	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113615	1.00[YRI][hapmap]
rs2194486	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241432	1.00[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs2288122	0.82[CHB][hapmap]
rs2303338	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2367200	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs311576	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs311578	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs311579	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs311585	0.81[ASN][1000 genomes]
rs311588	0.81[ASN][1000 genomes]
rs3731818	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3764949	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3764950	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821017	0.90[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4344936	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4610056	1.00[YRI][hapmap]
rs4832031	0.81[MKK][hapmap]
rs4832233	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs4832240	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4832263	0.93[MKK][hapmap];1.00[YRI][hapmap]
rs4832272	1.00[YRI][hapmap]
rs62147717	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6725046	0.86[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap]
rs6731358	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6749090	0.85[GIH][hapmap]
rs708600	1.00[LWK][hapmap];0.96[MKK][hapmap]
rs717144	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs718292	0.96[MKK][hapmap]
rs72847885	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7567380	0.91[ASN][1000 genomes]
rs7569654	1.00[YRI][hapmap]
rs7575430	0.86[AFR][1000 genomes]
rs9653508	0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv458574	chr2:86385728-86507688	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
21	nsv582372	chr2:86385728-86507688	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs965636	IMMT	cis	lymphoblastoid	seeQTL
rs965636	IMMT	cis	cerebellum	SCAN
rs965636	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs965636	MRPL35	cis	cerebellum	SCAN
rs965636	SH2D6	cis	cerebellum	SCAN
rs965636	MRPL35	cis	uninvolved skin	skin_eQTL
rs965636	MRPL35	cis	parietal	SCAN
rs965636	REEP1	cis	parietal	SCAN
rs965636	POLR1A	cis	cerebellum	SCAN
rs965636	MRPL35	cis	normal skin	skin_eQTL
rs965636	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs965636	IMMT	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86390400-86421200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:86393800-86413600	Weak transcription	Esophagus	oesophagus
3	chr2:86398600-86417200	Weak transcription	Fetal Brain Male	brain
4	chr2:86404000-86421200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:86406000-86421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:86407000-86415400	Weak transcription	Placenta	Placenta
7	chr2:86407000-86421200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:86407200-86413600	Weak transcription	Fetal Brain Female	brain
9	chr2:86407200-86414000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:86407200-86416600	Weak transcription	NHLF	lung
11	chr2:86407200-86417800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:86407200-86418600	Weak transcription	Ovary	ovary
13	chr2:86407200-86420800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:86407200-86421000	Weak transcription	Small Intestine	intestine
15	chr2:86407200-86421200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:86407600-86417000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:86408400-86417000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:86408400-86421000	Weak transcription	Brain Germinal Matrix	brain
19	chr2:86408600-86413600	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:86408600-86413600	Weak transcription	Fetal Stomach	stomach
21	chr2:86408600-86414200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:86408600-86414400	Weak transcription	HepG2	liver
23	chr2:86408600-86415400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:86408600-86415400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:86408600-86416600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:86408600-86416600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:86408600-86419000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:86408600-86420600	Weak transcription	NH-A	brain
29	chr2:86408600-86421000	Weak transcription	Fetal Intestine Large	intestine
30	chr2:86408600-86421200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:86410000-86415400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:86410400-86414400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr2:86410600-86414600	Weak transcription	Fetal Intestine Small	intestine
34	chr2:86411000-86414800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr2:86411200-86414000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:86411400-86414400	Enhancers	Primary B cells from peripheral blood	blood
37	chr2:86411600-86414000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:86411600-86414200	Enhancers	Fetal Thymus	thymus
39	chr2:86411600-86417000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:86411600-86421200	Weak transcription	Aorta	Aorta
41	chr2:86411800-86413600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr2:86411800-86413800	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr2:86411800-86413800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr2:86411800-86413800	Enhancers	Muscle Satellite Cultured Cells	--
45	chr2:86411800-86413800	Enhancers	Brain Angular Gyrus	brain
46	chr2:86411800-86416200	Enhancers	Fetal Heart	heart
47	chr2:86412000-86413800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:86412000-86413800	Enhancers	Adipose Nuclei	Adipose
49	chr2:86412000-86413800	Enhancers	Brain Cingulate Gyrus	brain
50	chr2:86412000-86413800	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links