Variant report

Variant	rs7641929
Chromosome Location	chr3:156529394-156529395
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr3:156529238-156529660	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:156529266-156529673	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr3:156529198-156529733	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:156529366-156529444	IMR90	lung:	n/a	n/a
5	STAT3	chr3:156529338-156529415	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr3:156529219-156529419	MCF10A-Er-Src	breast:	n/a	n/a
7	TCF12	chr3:156529210-156529856	SK-N-SH	brain:	n/a	n/a
8	MYC	chr3:156529173-156529570	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:156529281-156529769	PFSK-1	brain:	n/a	n/a
10	STAT3	chr3:156529057-156529691	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr3:156529370-156529651	IMR90	lung:	n/a	n/a
12	MYC	chr3:156529319-156529591	MCF10A-Er-Src	breast:	n/a	n/a
13	RAD21	chr3:156529324-156529616	IMR90	lung:	n/a	chr3:156529497-156529509
14	NR2F2	chr3:156528751-156529675	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156467361..156469859-chr3:156528012..156530054,3	MCF-7	breast:
2	chr3:156527949..156530289-chr3:156543460..156546861,3	K562	blood:
3	chr3:156529223..156530794-chr3:156884048..156887029,2	MCF-7	breast:
4	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
5	chr3:156392305..156394108-chr3:156527817..156529889,2	MCF-7	breast:
6	chr3:156527592..156531932-chr3:156540848..156546879,8	MCF-7	breast:

No data

Variant related genes	Relation type
PA2G4P4	TF binding region
ENSG00000240875	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10936037	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10936038	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711674	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717133	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492804	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497539	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072896	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13086516	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13097325	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430411	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560415	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560416	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1835372	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653817	0.83[YRI][hapmap]
rs344071	0.81[YRI][hapmap]
rs344072	0.81[YRI][hapmap]
rs344074	0.80[YRI][hapmap]
rs4680305	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59717073	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6776157	0.85[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9812169	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820830	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9837271	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842198	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858861	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9874866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS 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 target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7641929	LINC00886	cis	Artery Aorta	GTEx
rs7641929	LINC00886	cis	Stomach	GTEx
rs7641929	LINC00886	cis	Adipose Subcutaneous	GTEx
rs7641929	LINC00886	cis	Muscle Skeletal	GTEx
rs7641929	LINC00886	cis	Esophagus Mucosa	GTEx
rs7641929	LINC00886	cis	Thyroid	GTEx
rs7641929	LINC00886	cis	Esophagus Muscularis	GTEx
rs7641929	LINC00886	cis	lung	GTEx
rs7641929	LINC00886	cis	Artery Tibial	GTEx
rs7641929	LINC00886	cis	Nerve Tibial	GTEx
rs7641929	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156511400-156530400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:156518000-156529800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:156520200-156530400	Weak transcription	Right Ventricle	heart
4	chr3:156522200-156530400	Weak transcription	Gastric	stomach
5	chr3:156526200-156530600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:156526400-156530600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:156527000-156530400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:156527200-156533200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:156527400-156531600	Enhancers	Fetal Intestine Small	intestine
10	chr3:156527400-156533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:156527800-156533000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:156527800-156533800	Enhancers	HMEC	breast
13	chr3:156528200-156530000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:156528200-156533600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:156528400-156529400	Enhancers	Duodenum Mucosa	Duodenum
16	chr3:156528400-156530800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:156528400-156531000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr3:156528400-156531200	Enhancers	Fetal Intestine Large	intestine
19	chr3:156528400-156531200	Enhancers	HUVEC	blood vessel
20	chr3:156528400-156531200	Enhancers	NHDF-Ad	bronchial
21	chr3:156528400-156532800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:156528600-156529400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:156528600-156529400	Genic enhancers	GM12878-XiMat	blood
24	chr3:156528600-156530000	Enhancers	HSMMtube	muscle
25	chr3:156528600-156531200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:156528600-156531200	Enhancers	HepG2	liver
27	chr3:156528800-156529600	Enhancers	NHEK	skin
28	chr3:156528800-156530200	Weak transcription	Lung	lung
29	chr3:156528800-156530400	Weak transcription	Esophagus	oesophagus
30	chr3:156528800-156531600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:156528800-156531600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:156529000-156529400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:156529000-156529600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:156529000-156529600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:156529000-156529600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:156529000-156529800	Enhancers	Fetal Heart	heart
37	chr3:156529000-156529800	Enhancers	A549	lung
38	chr3:156529000-156530000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:156529000-156530000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr3:156529000-156530400	Weak transcription	Right Atrium	heart
41	chr3:156529000-156530400	Enhancers	Hela-S3	cervix
42	chr3:156529000-156530600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:156529000-156530600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:156529000-156530600	Weak transcription	Small Intestine	intestine
45	chr3:156529000-156531200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr3:156529000-156531200	Enhancers	Osteobl	bone
47	chr3:156529000-156531400	Enhancers	Liver	Liver
48	chr3:156529000-156531400	Enhancers	K562	blood
49	chr3:156529000-156531400	Enhancers	NH-A	brain
50	chr3:156529000-156531600	Enhancers	Primary T cells from cord blood	blood

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