Variant report

Variant	rs16827994
Chromosome Location	chr2:187388234-187388235
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	chr2:187386798..187388432-chr2:187393071..187395661,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10177153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10181681	0.92[EUR][1000 genomes]
rs10190003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10198525	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs10200749	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10497671	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs10497672	0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11675633	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11675656	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690758	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11692347	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11888432	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901465	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11903027	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13392819	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13394241	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13401304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428033	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1448848	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1448849	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1448855	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16827968	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1868383	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1869031	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2084488	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2197139	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2370688	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2887826	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35642346	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56137171	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61434493	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6434174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6709401	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6717525	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap]
rs6728382	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6731567	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs6744717	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72895449	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72897386	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72901315	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72901322	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579259	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7584137	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7603088	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917285	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv459988	chr2:187364878-187440683	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv584031	chr2:187364878-187440683	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16827994	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL
rs16827994	ITGAV	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187361400-187389200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:187363000-187408800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:187363200-187397600	Weak transcription	Small Intestine	intestine
4	chr2:187367200-187396800	Weak transcription	Gastric	stomach
5	chr2:187367200-187405800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:187371000-187389400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:187371000-187395800	Weak transcription	Fetal Heart	heart
8	chr2:187371000-187407800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:187372200-187390000	Weak transcription	Fetal Brain Male	brain
10	chr2:187373600-187395800	Weak transcription	HSMMtube	muscle
11	chr2:187373600-187397600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:187373800-187390200	Weak transcription	Brain Anterior Caudate	brain
13	chr2:187374000-187388600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:187374400-187389800	Weak transcription	Brain Germinal Matrix	brain
15	chr2:187374400-187396200	Weak transcription	Brain Substantia Nigra	brain
16	chr2:187374400-187398800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:187374800-187388400	Weak transcription	NHLF	lung
18	chr2:187377200-187397200	Weak transcription	HUVEC	blood vessel
19	chr2:187379000-187397400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:187380400-187389200	Weak transcription	Fetal Lung	lung
21	chr2:187381800-187406600	Weak transcription	NHEK	skin
22	chr2:187383000-187397000	Weak transcription	K562	blood
23	chr2:187383400-187388600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:187383400-187397600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:187384200-187397800	Weak transcription	A549	lung
26	chr2:187386200-187388400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:187386200-187388400	Weak transcription	Left Ventricle	heart
28	chr2:187386200-187388400	Weak transcription	Ovary	ovary
29	chr2:187386200-187388600	Weak transcription	Aorta	Aorta
30	chr2:187386200-187392600	Weak transcription	Thymus	Thymus
31	chr2:187386200-187395800	Weak transcription	NH-A	brain
32	chr2:187386200-187397000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:187386200-187397400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:187386200-187398400	Weak transcription	Liver	Liver
35	chr2:187386200-187405200	Weak transcription	HSMM	muscle
36	chr2:187386200-187408000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:187386400-187390200	Weak transcription	Fetal Intestine Large	intestine
38	chr2:187386600-187388400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:187386600-187389000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:187386600-187389000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:187386800-187388400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:187386800-187388400	Weak transcription	Primary T cells from cord blood	blood
43	chr2:187386800-187388400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:187386800-187388400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:187386800-187388600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:187386800-187388800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:187386800-187390000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:187386800-187390600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:187386800-187392000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:187386800-187397400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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