Variant report

Variant	rs12539942
Chromosome Location	chr7:6776585-6776586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:6767588..6769922-chr7:6774691..6777140,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187953	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10244591	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10272921	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10441131	0.81[ASN][1000 genomes]
rs10951994	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.83[ASN][1000 genomes]
rs12113879	0.81[ASN][1000 genomes]
rs12534591	0.83[EUR][1000 genomes]
rs12536067	0.81[AMR][1000 genomes]
rs12537448	1.00[JPT][hapmap]
rs12537487	0.80[AMR][1000 genomes]
rs12673800	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs13224907	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap]
rs13247186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28494902	0.86[ASN][1000 genomes]
rs28649084	0.81[ASN][1000 genomes]
rs2881352	0.91[JPT][hapmap]
rs34857592	0.80[ASN][1000 genomes]
rs34899283	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35121012	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35291651	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35644498	0.86[ASN][1000 genomes]
rs35768299	0.86[ASN][1000 genomes]
rs3757481	0.92[JPT][hapmap]
rs3801033	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs3801038	1.00[JPT][hapmap]
rs3801039	0.90[JPT][hapmap]
rs62439722	0.82[AMR][1000 genomes]
rs62439727	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62439737	0.85[ASN][1000 genomes]
rs6463576	0.89[CHD][hapmap];0.92[JPT][hapmap]
rs6463580	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6944332	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs6953825	1.00[JPT][hapmap]
rs6954172	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6971621	0.88[JPT][hapmap]
rs6974325	0.89[CHD][hapmap];0.92[JPT][hapmap]
rs6979127	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7779296	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7784521	0.85[ASN][1000 genomes]
rs7792579	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7792858	0.82[ASN][1000 genomes]
rs7796846	0.87[ASN][1000 genomes]
rs7798471	0.86[CHD][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap]
rs7804259	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs7804542	0.90[ASN][1000 genomes]
rs9639027	0.89[CHD][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv887439	chr7:6736332-6791749	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015646	chr7:6738483-6779270	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv887440	chr7:6743097-6820508	Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv887441	chr7:6744957-6919214	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	esv1819001	chr7:6746810-6785602	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv966754	chr7:6750289-6838266	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv887442	chr7:6753286-6820508	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv887443	chr7:6753286-6832265	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv887444	chr7:6753286-6855510	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv887445	chr7:6758018-6843722	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv887446	chr7:6758018-6870635	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv887447	chr7:6764583-6843722	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv887448	chr7:6764583-6855510	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv887449	chr7:6764583-6870635	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	esv2757207	chr7:6764583-6977214	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
17	esv2759504	chr7:6764583-6977214	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6770000-6783400	Weak transcription	Aorta	Aorta
2	chr7:6770200-6779000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:6770200-6779200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:6770200-6782600	Weak transcription	Small Intestine	intestine
5	chr7:6770400-6776800	Weak transcription	Pancreas	Pancrea
6	chr7:6770400-6777000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:6770400-6778400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:6770400-6784800	Weak transcription	NHLF	lung
9	chr7:6770800-6776800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:6770800-6777800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:6770800-6786400	Weak transcription	Fetal Brain Male	brain
12	chr7:6771000-6776800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:6771000-6776800	Weak transcription	NHDF-Ad	bronchial
14	chr7:6771000-6778200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:6771000-6778800	Weak transcription	Brain Hippocampus Middle	brain
16	chr7:6771000-6782000	Strong transcription	Fetal Stomach	stomach
17	chr7:6771000-6786200	Weak transcription	HUVEC	blood vessel
18	chr7:6771000-6786400	Weak transcription	Primary B cells from cord blood	blood
19	chr7:6771200-6776800	Weak transcription	Colonic Mucosa	Colon
20	chr7:6771200-6778600	Weak transcription	Fetal Heart	heart
21	chr7:6771200-6780200	Weak transcription	Right Atrium	heart
22	chr7:6771200-6781400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr7:6771200-6792400	Weak transcription	NHEK	skin
24	chr7:6771400-6776600	Weak transcription	Brain Germinal Matrix	brain
25	chr7:6771400-6777600	Strong transcription	Dnd41	blood
26	chr7:6771600-6781800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:6771800-6780400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:6771800-6783400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:6772000-6776800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:6772000-6777200	Strong transcription	Duodenum Mucosa	Duodenum
31	chr7:6772000-6777200	Strong transcription	HSMM	muscle
32	chr7:6772000-6777400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:6772000-6777400	Strong transcription	Primary T cells from cord blood	blood
34	chr7:6772000-6777400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr7:6772000-6777400	Strong transcription	Brain Anterior Caudate	brain
36	chr7:6772000-6777400	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr7:6772000-6777400	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr7:6772000-6777400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr7:6772000-6777400	Strong transcription	Thymus	Thymus
40	chr7:6772000-6777400	Strong transcription	A549	lung
41	chr7:6772000-6777600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr7:6772000-6777600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:6772000-6777600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr7:6772000-6777600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:6772000-6777800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr7:6772000-6777800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr7:6772000-6777800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:6772000-6777800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:6772000-6777800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:6772000-6777800	Strong transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links