Variant report

Variant	rs17826221
Chromosome Location	chr3:160160452-160160453
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160116116..160127665-chr3:160158037..160169627,42	K562	blood:
2	chr3:160158711..160161195-chr3:160357597..160359673,2	K562	blood:
3	chr3:160152431..160159028-chr3:160159168..160164097,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068885	Chromatin interaction
ENSG00000198987	Chromatin interaction
ENSG00000113810	Chromatin interaction
ENSG00000207779	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1047210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513551	0.85[CEU][hapmap]
rs10923	0.82[JPT][hapmap]
rs10936201	0.82[JPT][hapmap]
rs11706810	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708118	0.82[JPT][hapmap]
rs11709336	0.82[JPT][hapmap]
rs11718121	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719750	0.82[JPT][hapmap]
rs11720689	0.82[JPT][hapmap]
rs12632030	0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13403	0.85[CEU][hapmap]
rs1369666	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1451760	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1451761	0.85[CEU][hapmap]
rs1451762	0.85[CEU][hapmap]
rs17236473	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236544	0.81[CEU][hapmap]
rs17570467	0.81[CEU][hapmap]
rs1873076	0.81[JPT][hapmap]
rs1882126	0.81[CEU][hapmap]
rs1882127	0.81[CEU][hapmap]
rs1920664	0.81[CEU][hapmap]
rs1953506	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs1971128	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2279457	0.85[CEU][hapmap]
rs2305407	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs3732706	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773372	0.81[CEU][hapmap]
rs3851365	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3851366	0.85[CEU][hapmap]
rs4679654	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4679881	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs4679885	0.85[CEU][hapmap]
rs4679890	0.80[CEU][hapmap]
rs4679899	0.82[CEU][hapmap];0.80[JPT][hapmap]
rs4680576	0.85[CEU][hapmap]
rs4680579	0.85[CEU][hapmap]
rs4680580	0.85[CEU][hapmap]
rs4680585	0.85[CEU][hapmap]
rs4680588	0.85[CEU][hapmap]
rs4680589	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680591	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55992947	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56156703	0.84[EUR][1000 genomes]
rs56394279	0.82[AMR][1000 genomes]
rs6441313	0.85[CEU][hapmap]
rs6441314	0.85[CEU][hapmap]
rs6441319	0.81[CEU][hapmap]
rs6441320	0.85[CEU][hapmap]
rs6768975	0.81[CEU][hapmap]
rs6785881	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790951	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6791056	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6791261	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs6791567	0.80[YRI][hapmap]
rs6793560	0.88[CEU][hapmap];0.80[JPT][hapmap]
rs6798183	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6798668	0.81[CEU][hapmap]
rs6801300	0.82[JPT][hapmap]
rs6803828	0.86[CEU][hapmap]
rs6809153	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7355951	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7611130	0.85[CEU][hapmap]
rs7618974	0.81[CEU][hapmap]
rs7620828	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7621724	0.80[JPT][hapmap]
rs7624902	0.85[CEU][hapmap]
rs7627555	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7627756	0.81[CEU][hapmap]
rs7629	0.85[CEU][hapmap]
rs7631792	0.85[CEU][hapmap]
rs7634108	0.85[CEU][hapmap]
rs7634826	0.85[CEU][hapmap]
rs7643779	0.81[CEU][hapmap]
rs7647873	0.81[CEU][hapmap]
rs869467	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs869468	0.85[CEU][hapmap]
rs9968151	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17826221	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160120200-160164400	Weak transcription	Fetal Brain Male	brain
2	chr3:160122000-160161000	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:160122000-160164400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:160122000-160164600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:160130000-160166200	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:160133800-160164600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:160140800-160166600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:160142400-160164400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:160143600-160166600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:160145600-160166800	Weak transcription	Right Atrium	heart
11	chr3:160146000-160162400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:160146000-160164400	Weak transcription	Gastric	stomach
13	chr3:160146000-160165400	Weak transcription	Aorta	Aorta
14	chr3:160146000-160167000	Weak transcription	Pancreas	Pancrea
15	chr3:160146400-160166200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:160147000-160164400	Weak transcription	Esophagus	oesophagus
17	chr3:160147000-160166200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:160147800-160164400	Weak transcription	Lung	lung
19	chr3:160150000-160160600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:160150000-160162400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:160150400-160162400	Weak transcription	Spleen	Spleen
22	chr3:160150600-160166000	Weak transcription	Fetal Brain Female	brain
23	chr3:160151000-160160600	Weak transcription	Fetal Kidney	kidney
24	chr3:160151000-160166600	Weak transcription	Small Intestine	intestine
25	chr3:160151000-160166800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:160152000-160160600	Weak transcription	HepG2	liver
27	chr3:160152200-160163600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:160152200-160165200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:160152400-160164000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:160152400-160166000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:160152600-160165200	Weak transcription	Hela-S3	cervix
32	chr3:160152600-160166200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:160153200-160162400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:160153200-160166200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:160153400-160166600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:160154000-160163000	Weak transcription	HMEC	breast
37	chr3:160154000-160164600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:160154200-160162400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:160154200-160164400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:160154200-160165200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:160154200-160165400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:160154400-160162400	Weak transcription	Thymus	Thymus
43	chr3:160154400-160164400	Weak transcription	Brain Germinal Matrix	brain
44	chr3:160154600-160166400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:160155000-160165200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:160155000-160166600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:160155000-160167000	Weak transcription	Placenta	Placenta
48	chr3:160155200-160162400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:160155200-160162400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:160155200-160163000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links