Variant report

Variant	rs177083
Chromosome Location	chr2:32447718-32447719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32445227..32449129-chr2:32451328..32453997,4	K562	blood:
2	chr2:32444908..32446420-chr2:32446520..32449032,2	MCF-7	breast:
3	chr2:32427480..32429010-chr2:32446145..32448462,2	K562	blood:
4	chr2:32443634..32446548-chr2:32446914..32449802,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10172468	0.82[EUR][1000 genomes]
rs10208246	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs11124278	0.86[EUR][1000 genomes]
rs12465351	0.96[CEU][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs12997026	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs13427170	0.88[CEU][hapmap];0.88[GIH][hapmap];0.80[EUR][1000 genomes]
rs212686	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs212687	0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs212694	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs212695	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs212698	0.86[ASN][1000 genomes]
rs212699	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs212700	0.98[ASN][1000 genomes]
rs212701	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs212703	0.96[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs212704	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs212705	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs212706	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs212707	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs212708	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs212713	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212714	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.81[ASN][1000 genomes]
rs212721	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs212722	0.80[ASN][1000 genomes]
rs212723	0.80[ASN][1000 genomes]
rs212724	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs212726	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs212727	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.80[ASN][1000 genomes]
rs212728	0.80[ASN][1000 genomes]
rs212730	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs212731	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.80[ASN][1000 genomes]
rs212733	0.80[ASN][1000 genomes]
rs212734	0.80[ASN][1000 genomes]
rs212735	0.80[ASN][1000 genomes]
rs212737	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs212738	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs212740	0.80[EUR][1000 genomes]
rs212741	0.83[EUR][1000 genomes]
rs212743	0.85[EUR][1000 genomes]
rs212744	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs212748	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs212749	0.83[EUR][1000 genomes]
rs212752	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212753	0.88[EUR][1000 genomes]
rs212755	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs212756	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs212757	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212758	0.80[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs212759	0.80[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs212762	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs216544	0.91[GIH][hapmap]
rs2366736	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs430759	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4407291	0.84[EUR][1000 genomes]
rs4519572	0.84[EUR][1000 genomes]
rs455060	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs467523	0.84[CEU][hapmap];0.93[GIH][hapmap]
rs4952209	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs4952252	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs55877106	0.81[EUR][1000 genomes]
rs62134021	0.81[EUR][1000 genomes]
rs6716179	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6717209	0.96[CEU][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs7577696	0.82[GIH][hapmap]
rs7581432	0.96[CEU][hapmap];0.80[MEX][hapmap];0.82[EUR][1000 genomes]
rs7588883	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs7601267	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking 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 target site	39 gene(s)	inside rSNPs	diseases
6	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv2667	chr2:32444810-32489755	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs177083	EHD3	cis	parietal	SCAN
rs177083	NLRC4	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32391600-32452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:32391800-32453800	Weak transcription	Colonic Mucosa	Colon
3	chr2:32399200-32449600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:32403000-32452200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:32404200-32448000	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:32404200-32452400	Weak transcription	Right Ventricle	heart
7	chr2:32404200-32460600	Weak transcription	Esophagus	oesophagus
8	chr2:32404400-32450800	Weak transcription	Gastric	stomach
9	chr2:32404800-32447800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:32411600-32447800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:32412000-32450400	Weak transcription	Spleen	Spleen
12	chr2:32422000-32452400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:32423400-32448000	Weak transcription	Small Intestine	intestine
14	chr2:32424400-32455400	Weak transcription	Fetal Brain Male	brain
15	chr2:32426400-32455000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:32427400-32447800	Weak transcription	K562	blood
17	chr2:32433800-32451600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:32434600-32449800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:32435200-32451600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:32437800-32449000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:32438800-32452400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:32440800-32448800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:32442600-32448800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:32442800-32448800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr2:32442800-32452200	Strong transcription	Liver	Liver
26	chr2:32443000-32449800	Strong transcription	Fetal Intestine Large	intestine
27	chr2:32443000-32451600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:32443000-32483600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:32443200-32448600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:32443200-32451600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:32443200-32483800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:32444400-32451600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:32444600-32449400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:32444600-32451400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:32444600-32451400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:32444600-32452200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:32444800-32451600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:32444800-32451800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:32444800-32452600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:32444800-32452800	Weak transcription	Fetal Intestine Small	intestine
41	chr2:32445000-32449800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:32445200-32448800	Strong transcription	Left Ventricle	heart
43	chr2:32445200-32448800	Strong transcription	A549	lung
44	chr2:32445200-32449000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr2:32445200-32452600	Strong transcription	Placenta	Placenta
46	chr2:32445600-32448800	Strong transcription	Primary B cells from cord blood	blood
47	chr2:32445800-32447800	Weak transcription	HSMMtube	muscle
48	chr2:32445800-32451000	Weak transcription	Fetal Stomach	stomach
49	chr2:32445800-32452200	Weak transcription	Fetal Heart	heart
50	chr2:32445800-32452400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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