Variant report

Variant	rs6840258
Chromosome Location	chr4:87973668-87973669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87926523..87929308-chr4:87972685..87974681,2	MCF-7	breast:
2	chr4:87973183..87975185-chr4:87980947..87982650,2	MCF-7	breast:
3	chr4:87856023..87858203-chr4:87973033..87975111,2	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10023056	0.85[CEU][hapmap]
rs10032244	0.89[CEU][hapmap]
rs10032710	0.89[CEU][hapmap]
rs10516785	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10516786	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs10516788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1471251	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs151451	0.88[CEU][hapmap]
rs17012200	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs17012234	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17012334	0.85[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs17604480	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17701999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17752307	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1842685	0.89[CEU][hapmap]
rs2061498	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs236676	0.83[CEU][hapmap]
rs340633	0.84[CEU][hapmap]
rs340637	0.90[CEU][hapmap]
rs340638	0.89[CEU][hapmap]
rs340642	0.90[CEU][hapmap]
rs340643	0.89[CEU][hapmap]
rs340650	0.90[CEU][hapmap]
rs3733377	0.89[CEU][hapmap]
rs3755980	0.83[CEU][hapmap]
rs4693801	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55787557	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55816619	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55879154	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55982755	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56023922	0.81[ASN][1000 genomes]
rs56050898	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56201818	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56390363	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56395939	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56406125	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819155	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6839933	0.89[CEU][hapmap]
rs6854749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667747	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72667748	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72667750	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72667751	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667752	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667753	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667754	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667757	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72667759	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72667765	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7665282	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap]
rs767315	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7682652	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7695426	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87960400-87975400	Weak transcription	Brain Germinal Matrix	brain
2	chr4:87961000-87979200	Weak transcription	HSMMtube	muscle
3	chr4:87963200-87982200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:87964600-87995000	Weak transcription	Hela-S3	cervix
5	chr4:87964800-87979200	Weak transcription	A549	lung
6	chr4:87966200-87979200	Weak transcription	NH-A	brain
7	chr4:87967000-87975000	Strong transcription	Dnd41	blood
8	chr4:87967600-87975000	Weak transcription	Stomach Mucosa	stomach
9	chr4:87967800-87974600	Strong transcription	Fetal Intestine Large	intestine
10	chr4:87968600-87974400	Enhancers	Colon Smooth Muscle	Colon
11	chr4:87968600-87975400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:87968600-87979000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:87968800-87973800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:87968800-87973800	Weak transcription	Small Intestine	intestine
15	chr4:87968800-87975000	Weak transcription	Gastric	stomach
16	chr4:87968800-87975400	Weak transcription	Spleen	Spleen
17	chr4:87968800-87975600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:87968800-87975800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr4:87968800-87975800	Weak transcription	NHEK	skin
20	chr4:87968800-87975800	Weak transcription	NHLF	lung
21	chr4:87968800-87976200	Weak transcription	NHDF-Ad	bronchial
22	chr4:87968800-87977600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:87968800-87978800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:87968800-87979000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:87968800-87979200	Weak transcription	HMEC	breast
26	chr4:87968800-87979200	Weak transcription	HSMM	muscle
27	chr4:87968800-87979400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:87968800-87979400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:87968800-87980000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:87968800-87982000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr4:87968800-87982200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:87968800-87983400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:87968800-87995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:87969000-87974200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:87969000-87975000	Weak transcription	Esophagus	oesophagus
36	chr4:87969000-87976000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:87969000-87994600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:87969200-87974200	Weak transcription	Fetal Kidney	kidney
39	chr4:87969200-87974800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:87969200-87974800	Weak transcription	Fetal Muscle Leg	muscle
41	chr4:87969400-87974200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr4:87969600-87974600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:87970000-87973800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:87970000-87974000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:87970000-87974800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:87970000-87976000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:87970200-87974800	Weak transcription	Fetal Lung	lung
48	chr4:87970200-87975000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:87970200-87975800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:87970200-87976600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links