Variant report

Variant	rs2017146
Chromosome Location	chr4:143538179-143538180
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:143488759..143491260-chr4:143536558..143538874,2	MCF-7	breast:
2	chr4:143385183..143386744-chr4:143537618..143539562,2	MCF-7	breast:
3	chr4:143535928..143538576-chr4:143767240..143768815,2	MCF-7	breast:
4	chr4:143469197..143474225-chr4:143534708..143538333,6	MCF-7	breast:
5	chr4:143536517..143538495-chr4:143637512..143640289,2	MCF-7	breast:
6	chr4:143388945..143399475-chr4:143525396..143540220,51	MCF-7	breast:
7	chr4:143536781..143539215-chr4:143551772..143553795,2	MCF-7	breast:
8	chr4:143520357..143522520-chr4:143535203..143538604,3	MCF-7	breast:
9	chr4:143469254..143471063-chr4:143535925..143538743,3	MCF-7	breast:
10	chr4:143517546..143521080-chr4:143535706..143539870,4	MCF-7	breast:
11	chr4:143420095..143422300-chr4:143536470..143540708,3	MCF-7	breast:
12	chr4:143387939..143398265-chr4:143528932..143544358,55	MCF-7	breast:
13	chr4:143537607..143539576-chr4:143628828..143631506,2	MCF-7	breast:
14	chr4:143535273..143539133-chr4:143641663..143644812,3	MCF-7	breast:
15	chr4:143535588..143538325-chr4:143625041..143627552,2	MCF-7	breast:
16	chr4:143537049..143539439-chr4:143765970..143768416,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1031104	0.83[CHD][hapmap];0.89[MEX][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs10857397	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857399	0.81[JPT][hapmap]
rs11100754	0.80[ASN][1000 genomes]
rs1116690	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11723809	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11942731	0.81[YRI][hapmap]
rs11943397	0.81[ASW][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11944455	0.91[CHB][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12500698	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12644329	0.80[ASN][1000 genomes]
rs13102191	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13109603	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13109664	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13114452	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13119090	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13125362	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13125853	0.96[ASN][1000 genomes]
rs13133181	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1364921	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364922	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1364923	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1364925	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1373041	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1443185	0.81[ASN][1000 genomes]
rs1443186	0.81[ASN][1000 genomes]
rs1443191	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1473222	0.83[CEU][hapmap];0.92[CHB][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1899565	0.83[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs2083781	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2120158	0.81[ASW][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs2165820	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2197216	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2217017	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2874870	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2874871	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975311	0.83[CEU][hapmap];0.92[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61371792	0.82[ASN][1000 genomes]
rs6537123	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6830053	0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs6830886	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6831966	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6839894	0.90[CHB][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7434705	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7441478	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7680076	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7680631	0.84[ASN][1000 genomes]
rs7695514	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7698691	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs978361	0.83[CHD][hapmap]
rs979194	0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs979195	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs979196	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461660	chr4:143437219-143538179	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv595605	chr4:143437219-143538179	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv830101	chr4:143518810-143684392	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143517400-143539400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:143531200-143538600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:143532600-143540200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:143534000-143538400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:143534000-143538600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:143534200-143538600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:143536800-143538400	Weak transcription	Aorta	Aorta
8	chr4:143537000-143538400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:143537000-143575800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:143537200-143539400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:143537400-143538400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:143537400-143538400	Weak transcription	Left Ventricle	heart
13	chr4:143537400-143540600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:143537600-143539000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
15	chr4:143537800-143538600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
16	chr4:143538000-143541800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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