Variant report

Variant	rs10239139
Chromosome Location	chr7:3000424-3000425
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	chr7:2996961..2999238-chr7:2999589..3002363,2	MCF-7	breast:
2	chr7:2995128..2998225-chr7:3000156..3002896,4	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10085734	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10223941	0.83[AMR][1000 genomes]
rs10248838	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10270253	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10277523	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4422691	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4513879	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4549680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58172300	1.00[AMR][1000 genomes]
rs6953177	0.85[AMR][1000 genomes]
rs6968463	0.85[AMR][1000 genomes]
rs6972349	0.85[AMR][1000 genomes]
rs6977052	0.85[AMR][1000 genomes]
rs73287239	1.00[AMR][1000 genomes]
rs7790861	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7795713	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1022938	chr7:2899514-3131881	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv605873	chr7:2920067-3204177	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1025727	chr7:2938301-3064008	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS 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	4 gene(s)	inside rSNPs	diseases
5	nsv1026476	chr7:2965034-3311344	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv538656	chr7:2965034-3311344	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv464260	chr7:2966138-3315572	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv605874	chr7:2966138-3315572	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1018287	chr7:2967524-3298539	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv538657	chr7:2967524-3298539	Bivalent/Poised TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2992200-3000600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr7:2997000-3006000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:2997200-3002400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr7:2997200-3002400	Weak transcription	NHEK	skin
5	chr7:2997200-3005600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:2998600-3005400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:2998800-3000800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr7:2998800-3002800	Weak transcription	Primary B cells from cord blood	blood
9	chr7:2999000-3000600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr7:2999000-3000600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr7:2999000-3001000	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr7:2999000-3001200	Weak transcription	Fetal Intestine Small	intestine
13	chr7:2999000-3004000	Weak transcription	GM12878-XiMat	blood
14	chr7:2999000-3005400	Weak transcription	Spleen	Spleen
15	chr7:2999400-3005000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr7:2999400-3005400	Weak transcription	Thymus	Thymus
17	chr7:2999600-3002400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:2999800-3002600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:2999800-3005200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:2999800-3005400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:3000000-3001400	Weak transcription	Fetal Thymus	thymus
22	chr7:3000000-3002400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:3000000-3005400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:3000200-3000600	Enhancers	Primary T cells from cord blood	blood
25	chr7:3000200-3000600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr7:3000200-3001400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:3000400-3000800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr7:3000400-3001400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr7:3000400-3001600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr7:3000400-3002600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr7:3000400-3002800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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