Variant report

Variant	rs2158639
Chromosome Location	chr7:6219643-6219644
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr7:6219209-6219758	GM12878	blood:	n/a	n/a
2	RUNX3	chr7:6219210-6219747	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:6219262-6219727	GM12892	blood:	n/a	n/a
4	RUNX3	chr7:6219213-6219759	GM12878	blood:	n/a	n/a
5	STAT5A	chr7:6219295-6219687	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:6219241-6219770	GM12878	blood:	n/a	n/a
7	POU2F2	chr7:6219121-6219689	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6218147..6221120-chr7:6228782..6230937,2	K562	blood:
2	chr7:6218606..6220870-chr7:6221608..6224253,2	K562	blood:
3	chr7:6217036..6219726-chr7:6310745..6313246,2	K562	blood:

Variant related genes	Relation type
CYTH3	TF binding region
ENSG00000238534	TF binding region
ENSG00000008256	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10249091	0.93[EUR][1000 genomes]
rs10281120	0.93[EUR][1000 genomes]
rs12666407	0.86[EUR][1000 genomes]
rs12667859	0.86[EUR][1000 genomes]
rs12671407	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17188097	0.87[AMR][1000 genomes]
rs1964219	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2098800	0.91[AMR][1000 genomes]
rs3750065	0.93[EUR][1000 genomes]
rs3828952	0.86[EUR][1000 genomes]
rs57081447	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57153401	0.87[EUR][1000 genomes]
rs852151	1.00[YRI][hapmap]
rs9791591	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv5629	chr7:6217866-6263131	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6198800-6220000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:6201800-6226400	Weak transcription	Liver	Liver
3	chr7:6202000-6230600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:6202400-6226600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr7:6202400-6238000	Weak transcription	Fetal Kidney	kidney
6	chr7:6202600-6228200	Weak transcription	Dnd41	blood
7	chr7:6204600-6228000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr7:6207800-6229800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:6209600-6230000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:6210000-6230000	Weak transcription	Brain Substantia Nigra	brain
11	chr7:6210600-6228000	Weak transcription	Thymus	Thymus
12	chr7:6210800-6229600	Weak transcription	Colonic Mucosa	Colon
13	chr7:6210800-6230000	Strong transcription	Fetal Stomach	stomach
14	chr7:6211000-6226200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:6211800-6237800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:6212000-6220400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr7:6212200-6237800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:6212600-6220800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:6212600-6231000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:6212800-6238200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:6213000-6231200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:6213200-6219800	Weak transcription	Esophagus	oesophagus
23	chr7:6213200-6240600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:6215800-6220600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:6215800-6220600	Weak transcription	HUVEC	blood vessel
26	chr7:6215800-6220800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr7:6215800-6231400	Weak transcription	Hela-S3	cervix
28	chr7:6216200-6220400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:6216400-6220200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:6216400-6225200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:6216800-6223200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:6216800-6229600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:6216800-6237000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:6216800-6237800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr7:6217200-6226000	Weak transcription	A549	lung
36	chr7:6217400-6221200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr7:6217400-6222200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:6217400-6226000	Weak transcription	Primary B cells from cord blood	blood
39	chr7:6217400-6227600	Weak transcription	Fetal Lung	lung
40	chr7:6217600-6219800	Enhancers	Pancreas	Pancrea
41	chr7:6217600-6226000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:6217600-6226200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:6217600-6226600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:6217600-6228600	Weak transcription	Brain Germinal Matrix	brain
45	chr7:6217600-6231600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr7:6217800-6219800	Enhancers	Right Ventricle	heart
47	chr7:6217800-6219800	Enhancers	NHDF-Ad	bronchial
48	chr7:6217800-6220000	Enhancers	Gastric	stomach
49	chr7:6217800-6222400	Weak transcription	Fetal Intestine Large	intestine
50	chr7:6217800-6225800	Weak transcription	Fetal Brain Female	brain

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