Variant report

Variant	rs10006958
Chromosome Location	chr4:129753660-129753661
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	chr4:129753454..129755745-chr4:129760816..129762452,2	MCF-7	breast:
2	chr4:129731357..129734214-chr4:129752200..129753715,2	K562	blood:

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10008441	0.85[AFR][1000 genomes]
rs10015538	0.88[AFR][1000 genomes]
rs10026447	0.88[AFR][1000 genomes]
rs28430630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28434631	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28583676	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28624232	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28707598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9307610	0.88[AFR][1000 genomes]
rs9991702	0.88[AFR][1000 genomes]
rs9996611	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
2	chr4:129746600-129761800	Strong transcription	Dnd41	blood
3	chr4:129746800-129757000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:129746800-129770200	Weak transcription	HMEC	breast
5	chr4:129747000-129766600	Weak transcription	NHEK	skin
6	chr4:129747400-129754200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr4:129747400-129756600	Weak transcription	Esophagus	oesophagus
8	chr4:129747400-129761600	Weak transcription	Placenta	Placenta
9	chr4:129748000-129761600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:129749000-129754200	Genic enhancers	H1 Cell Line	embryonic stem cell
11	chr4:129751600-129753800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:129751600-129754000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:129751600-129754200	Enhancers	Small Intestine	intestine
14	chr4:129751600-129754800	Enhancers	Pancreas	Pancrea
15	chr4:129751600-129757200	Genic enhancers	Fetal Intestine Small	intestine
16	chr4:129751800-129754000	Enhancers	Brain Hippocampus Middle	brain
17	chr4:129751800-129754000	Enhancers	Colon Smooth Muscle	Colon
18	chr4:129751800-129754200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:129751800-129754200	Enhancers	Liver	Liver
20	chr4:129751800-129754200	Enhancers	Fetal Intestine Large	intestine
21	chr4:129751800-129754200	Enhancers	Fetal Stomach	stomach
22	chr4:129752000-129754200	Enhancers	Rectal Smooth Muscle	rectum
23	chr4:129752200-129754000	Strong transcription	Hela-S3	cervix
24	chr4:129752200-129756400	Weak transcription	Spleen	Spleen
25	chr4:129752400-129753800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:129752400-129754200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr4:129752400-129758000	Strong transcription	Primary T cells from cord blood	blood
28	chr4:129752400-129758600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:129752400-129763800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:129752600-129753800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:129752600-129754000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
32	chr4:129752600-129755200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr4:129752600-129756800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:129752600-129757200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr4:129752600-129761800	Strong transcription	Fetal Thymus	thymus
36	chr4:129752800-129754000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
37	chr4:129752800-129755600	Strong transcription	Fetal Muscle Trunk	muscle
38	chr4:129752800-129755600	Strong transcription	HSMM	muscle
39	chr4:129752800-129756000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:129752800-129756000	Weak transcription	Lung	lung
41	chr4:129752800-129756800	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr4:129752800-129758200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:129752800-129758200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:129752800-129760600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:129753000-129753800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:129753000-129753800	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr4:129753000-129753800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr4:129753000-129754000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:129753000-129754000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr4:129753000-129754000	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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