Variant report

Variant	rs12702461
Chromosome Location	chr7:6033469-6033470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:6033194..6036666-chr7:6097186..6100537,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086232	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12112229	0.85[ASN][1000 genomes]
rs12702460	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702462	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702463	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702464	0.98[ASN][1000 genomes]
rs12702468	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13240138	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13245536	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13311041	0.85[EUR][1000 genomes]
rs1860462	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1986625	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2009115	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2286680	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34197105	0.98[ASN][1000 genomes]
rs3735296	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3779107	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59901370	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6463525	0.95[ASN][1000 genomes]
rs6949598	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953340	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6964944	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6974270	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71524066	0.83[EUR][1000 genomes]
rs7788051	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7793254	0.85[ASN][1000 genomes]
rs7799214	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7805798	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
2	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
3	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
5	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
6	nsv1034215	chr7:5748982-6056619	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
7	nsv1016690	chr7:5749222-6056619	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
8	nsv1027679	chr7:5760731-6056619	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
10	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription 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	138 gene(s)	inside rSNPs	diseases
11	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
12	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
13	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
14	nsv433017	chr7:5853557-6045391	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv830894	chr7:5889658-6072215	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
16	nsv1034916	chr7:5934780-6158970	Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
17	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
18	nsv933765	chr7:6029095-6039048	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6010400-6048000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:6015800-6033600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:6016200-6047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:6016600-6033800	Weak transcription	GM12878-XiMat	blood
5	chr7:6017000-6035000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:6017400-6038600	Weak transcription	Brain Angular Gyrus	brain
7	chr7:6018000-6033600	Weak transcription	HUVEC	blood vessel
8	chr7:6018200-6034400	Weak transcription	K562	blood
9	chr7:6018200-6035000	Weak transcription	NH-A	brain
10	chr7:6018400-6035400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:6019400-6035400	Weak transcription	HepG2	liver
12	chr7:6019600-6035200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:6019600-6035200	Weak transcription	Fetal Brain Male	brain
14	chr7:6022600-6048000	Weak transcription	NHLF	lung
15	chr7:6023600-6035000	Weak transcription	HSMMtube	muscle
16	chr7:6025000-6035400	Weak transcription	Psoas Muscle	Psoas
17	chr7:6025000-6039600	Weak transcription	Esophagus	oesophagus
18	chr7:6025000-6048000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:6025200-6035000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:6025200-6046800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:6025400-6035200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:6025400-6035200	Weak transcription	HSMM	muscle
23	chr7:6025800-6038600	Weak transcription	Aorta	Aorta
24	chr7:6025800-6045200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:6026200-6042800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:6026200-6045400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:6026200-6046200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:6026400-6033600	Strong transcription	Dnd41	blood
29	chr7:6026400-6034800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:6026400-6036000	Strong transcription	Adipose Nuclei	Adipose
31	chr7:6026400-6036800	Strong transcription	Liver	Liver
32	chr7:6026400-6037200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:6026400-6040000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:6026400-6042000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:6026400-6043600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:6026400-6043600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr7:6026400-6043600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr7:6026400-6044000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:6026400-6044000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:6026400-6045000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr7:6026400-6045000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:6026400-6045400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:6026400-6045600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:6026600-6034800	Weak transcription	Pancreas	Pancrea
45	chr7:6026600-6035000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr7:6026600-6042800	Strong transcription	Fetal Stomach	stomach
47	chr7:6026600-6045400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr7:6026800-6035400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr7:6027200-6034800	Weak transcription	Colonic Mucosa	Colon
50	chr7:6027400-6033600	Weak transcription	Brain Germinal Matrix	brain

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