Variant report

Variant	rs6531944
Chromosome Location	chr4:87921241-87921242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87853540..87856355-chr4:87919742..87922210,3	MCF-7	breast:
2	chr4:87918478..87926067-chr4:87926181..87931063,13	MCF-7	breast:
3	chr4:87853601..87856121-chr4:87920561..87922700,3	K562	blood:
4	chr4:87852916..87856061-chr4:87919493..87922700,3	K562	blood:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10003332	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10008600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10022960	0.92[ASN][1000 genomes]
rs1374936	0.83[ASN][1000 genomes]
rs1374937	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1584345	0.90[CHB][hapmap]
rs168161	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012291	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1972969	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2053774	0.91[ASN][1000 genomes]
rs2272777	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2594276	0.83[CHB][hapmap]
rs2705617	0.83[ASN][1000 genomes]
rs340627	0.97[ASN][1000 genomes]
rs340628	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340629	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340632	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs340635	1.00[ASN][1000 genomes]
rs340640	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340644	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340645	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340646	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs340649	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340652	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4536897	0.89[ASW][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4693155	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][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]
rs4693797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4693799	1.00[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]
rs58317309	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6531943	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531945	1.00[CHB][hapmap];0.88[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]
rs6531947	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815546	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6848056	0.92[ASN][1000 genomes]
rs6853011	0.92[ASN][1000 genomes]
rs72876089	0.89[EUR][1000 genomes]
rs73837575	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7685248	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs895740	0.83[ASN][1000 genomes]
rs965824	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6531944	Hs.480174	cis	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87899200-87922800	Weak transcription	Osteobl	bone
3	chr4:87899200-87925800	Weak transcription	Hela-S3	cervix
4	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:87900000-87924400	Weak transcription	NHEK	skin
6	chr4:87903200-87926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:87904200-87926200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:87914200-87927400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:87916000-87926200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:87916200-87922800	Weak transcription	Lung	lung
11	chr4:87916200-87927200	Weak transcription	Esophagus	oesophagus
12	chr4:87916400-87926200	Weak transcription	Fetal Intestine Large	intestine
13	chr4:87916400-87927200	Weak transcription	Gastric	stomach
14	chr4:87917800-87921600	Enhancers	Primary B cells from cord blood	blood
15	chr4:87917800-87921800	Enhancers	Primary B cells from peripheral blood	blood
16	chr4:87918000-87925400	Enhancers	Placenta	Placenta
17	chr4:87918800-87921600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:87919000-87921600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr4:87919000-87921600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr4:87919000-87927000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr4:87919200-87921600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr4:87919200-87921800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:87919200-87922000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr4:87919200-87922200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:87919200-87927400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:87919400-87921600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr4:87919400-87921600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr4:87919400-87923000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:87919400-87925400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr4:87919600-87922200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:87919800-87921600	Enhancers	GM12878-XiMat	blood
32	chr4:87919800-87922200	Enhancers	Colon Smooth Muscle	Colon
33	chr4:87919800-87923400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr4:87920000-87921600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:87920000-87921600	Enhancers	H9 Cell Line	embryonic stem cell
36	chr4:87920000-87921600	Enhancers	Fetal Thymus	thymus
37	chr4:87920000-87921600	Enhancers	Rectal Smooth Muscle	rectum
38	chr4:87920000-87921600	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr4:87920000-87921600	Enhancers	Dnd41	blood
40	chr4:87920000-87921600	Enhancers	K562	blood
41	chr4:87920000-87922000	Enhancers	Duodenum Mucosa	Duodenum
42	chr4:87920000-87922400	Enhancers	Liver	Liver
43	chr4:87920000-87923000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr4:87920000-87923400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr4:87920200-87921400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:87920200-87921600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:87920200-87921600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:87920200-87922200	Enhancers	Fetal Lung	lung
49	chr4:87920200-87923600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:87920400-87922600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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