Variant report

Variant	rs836488
Chromosome Location	chr7:6419793-6419794
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	chr7:6412400..6417963-chr7:6418207..6425853,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136238	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1647224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2272154	0.83[CHB][hapmap]
rs2303364	0.90[JPT][hapmap]
rs35190087	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35235058	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5020305	0.83[CHB][hapmap]
rs702482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs836474	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836479	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs836486	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836490	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs836493	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs836510	0.95[CHB][hapmap]
rs836518	0.95[CHB][hapmap]
rs836523	0.95[CHB][hapmap]
rs836532	0.95[CHB][hapmap]
rs836547	0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs836560	0.95[CHB][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv605999	chr7:6396719-6472881	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv967451	chr7:6417630-6427589	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6415600-6423800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:6415800-6422400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:6415800-6422600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:6415800-6427400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:6416000-6424800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:6416200-6421200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:6416200-6422600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:6416400-6420600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:6416400-6422400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:6416600-6423800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:6417000-6421800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr7:6417000-6422400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:6417000-6427400	Weak transcription	Thymus	Thymus
14	chr7:6417200-6419800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:6417200-6419800	Enhancers	Ovary	ovary
16	chr7:6417200-6421400	Enhancers	Psoas Muscle	Psoas
17	chr7:6417200-6422600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:6417200-6426400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:6417200-6435400	Weak transcription	Fetal Brain Male	brain
20	chr7:6417400-6421600	Weak transcription	Esophagus	oesophagus
21	chr7:6417600-6422400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:6417600-6423000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:6417800-6419800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr7:6417800-6419800	Weak transcription	Fetal Heart	heart
25	chr7:6417800-6419800	Genic enhancers	Fetal Intestine Large	intestine
26	chr7:6417800-6420400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr7:6417800-6420600	Weak transcription	Gastric	stomach
28	chr7:6417800-6422200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr7:6417800-6422400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr7:6417800-6422600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr7:6417800-6423800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:6417800-6423800	Weak transcription	Fetal Lung	lung
33	chr7:6417800-6424800	Weak transcription	Brain Germinal Matrix	brain
34	chr7:6417800-6425400	Weak transcription	Fetal Brain Female	brain
35	chr7:6418400-6420600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr7:6418600-6419800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr7:6418600-6423800	Enhancers	Primary B cells from peripheral blood	blood
38	chr7:6418600-6425200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr7:6418800-6419800	Genic enhancers	Duodenum Mucosa	Duodenum
40	chr7:6418800-6419800	Genic enhancers	Fetal Muscle Leg	muscle
41	chr7:6418800-6420400	Genic enhancers	Primary B cells from cord blood	blood
42	chr7:6418800-6422400	Strong transcription	Fetal Intestine Small	intestine
43	chr7:6419000-6419800	Genic enhancers	Primary T cells from cord blood	blood
44	chr7:6419000-6419800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr7:6419000-6419800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:6419000-6419800	Genic enhancers	Placenta	Placenta
47	chr7:6419000-6419800	Enhancers	Small Intestine	intestine
48	chr7:6419000-6420000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr7:6419000-6420000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr7:6419000-6420400	Enhancers	Brain Angular Gyrus	brain

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