Variant report

Variant	rs6710613
Chromosome Location	chr2:38840068-38840069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38838797..38841106-chr2:38843621..38847033,3	MCF-7	breast:
2	chr2:38838600..38841339-chr2:38925326..38927602,2	K562	blood:
3	chr2:38838640..38841229-chr2:38869315..38872620,3	K562	blood:
4	chr2:38839551..38842960-chr2:38892269..38895636,5	K562	blood:
5	chr2:38830091..38832083-chr2:38838036..38840443,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143891	Chromatin interaction
ENSG00000143889	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1543881	0.90[YRI][hapmap];0.81[AMR][1000 genomes]
rs17022945	0.81[YRI][hapmap]
rs17576044	0.89[YRI][hapmap]
rs17603782	0.94[YRI][hapmap];0.81[AMR][1000 genomes]
rs41446253	0.81[YRI][hapmap]
rs55773228	0.83[AFR][1000 genomes]
rs6748685	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907906	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907918	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73929052	0.81[AMR][1000 genomes]
rs7580657	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7584862	0.89[YRI][hapmap]
rs7594264	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
7	nsv581485	chr2:38839323-38893660	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38831200-38840400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:38831200-38840600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:38831400-38840800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:38835200-38840400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:38835200-38843400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:38835400-38842000	Weak transcription	HMEC	breast
7	chr2:38835400-38842200	Weak transcription	NHEK	skin
8	chr2:38835400-38843400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:38835400-38862400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:38837800-38842400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr2:38838200-38840200	Enhancers	Primary T cells fromperipheralblood	blood
12	chr2:38838600-38840600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:38838600-38840600	Enhancers	K562	blood
14	chr2:38838600-38842200	Enhancers	Stomach Mucosa	stomach
15	chr2:38838600-38845000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:38839000-38840200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:38839000-38842000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:38839000-38847200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:38839200-38840200	Enhancers	GM12878-XiMat	blood
20	chr2:38839200-38841800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:38839200-38842600	Enhancers	HepG2	liver
22	chr2:38839400-38841200	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr2:38839400-38842200	Enhancers	Primary hematopoietic stem cells	blood
24	chr2:38839600-38840200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:38839600-38841000	Enhancers	HSMM	muscle
26	chr2:38839600-38841400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:38839800-38840400	Enhancers	Osteobl	bone
28	chr2:38839800-38840600	Enhancers	NHDF-Ad	bronchial
29	chr2:38839800-38841000	Enhancers	HSMMtube	muscle
30	chr2:38839800-38841200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr2:38839800-38843400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr2:38840000-38840200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:38840000-38840200	Enhancers	Duodenum Mucosa	Duodenum
34	chr2:38840000-38840800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:38840000-38840800	Weak transcription	Adipose Nuclei	Adipose
36	chr2:38840000-38841000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:38840000-38841000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:38840000-38841000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:38840000-38841200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr2:38840000-38841200	Enhancers	NHLF	lung
41	chr2:38840000-38841800	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links