Variant report

Variant	rs6747638
Chromosome Location	chr2:113421975-113421976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113421512..113426143-chr2:113441172..113445759,7	K562	blood:
2	chr2:113420962..113423174-chr2:113470482..113472440,2	K562	blood:
3	chr2:113420288..113422863-chr2:113448665..113451519,3	MCF-7	breast:
4	chr2:113420362..113422891-chr2:113448382..113450135,2	MCF-7	breast:
5	chr2:113421228..113422950-chr2:113462402..113464448,2	K562	blood:
6	chr2:113419485..113422218-chr2:113423311..113426993,3	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10177499	0.94[EUR][1000 genomes]
rs10199279	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1061254	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10746527	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10779886	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11123144	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12994441	0.81[EUR][1000 genomes]
rs12996187	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13023311	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17042199	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs2312699	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34109218	0.88[EUR][1000 genomes]
rs3936697	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4630766	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4848286	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4849087	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4849088	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4849089	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4849090	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4849092	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849093	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4849094	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4849095	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4849096	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4849100	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56092429	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61443276	0.86[EUR][1000 genomes]
rs6737094	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6747928	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6751117	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6793	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72948491	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7558138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7559775	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs885346	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6747638	AC079922.3	cis	Esophagus Mucosa	GTEx
rs6747638	AC079922.3	cis	Heart Left Ventricle	GTEx
rs6747638	AC079922.3	cis	Esophagus Muscularis	GTEx
rs6747638	AC079922.3	cis	Nerve Tibial	GTEx
rs6747638	AC079922.3	cis	Artery Tibial	GTEx
rs6747638	AC079922.3	cis	lung	GTEx
rs6747638	AC079922.3	cis	Muscle Skeletal	GTEx
rs6747638	AC079922.3	cis	Adipose Subcutaneous	GTEx
rs6747638	AC079922.3	cis	Artery Aorta	GTEx
rs6747638	AC079922.3	cis	Whole Blood	GTEx
rs6747638	AC079922.3	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113405000-113423200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:113405200-113423200	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr2:113405200-113423800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr2:113405400-113422600	Strong transcription	Primary B cells from peripheral blood	blood
5	chr2:113405400-113423200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:113405400-113423200	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:113405600-113422000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:113405800-113422600	Strong transcription	Fetal Muscle Leg	muscle
9	chr2:113406000-113423000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:113406200-113423400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:113406200-113423400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:113406200-113423600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:113406200-113424600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:113406400-113423000	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr2:113406400-113423000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:113406400-113423200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr2:113406800-113423200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:113407000-113423000	Strong transcription	NHDF-Ad	bronchial
19	chr2:113407000-113423200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:113407000-113423200	Strong transcription	Fetal Thymus	thymus
21	chr2:113407000-113423200	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:113407000-113423400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:113407000-113423400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr2:113407400-113422800	Strong transcription	HSMMtube	muscle
25	chr2:113407600-113422200	Strong transcription	HSMM	muscle
26	chr2:113407600-113422600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:113407600-113422800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:113408200-113423000	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:113408400-113422800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:113408600-113422200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:113408800-113422600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:113409200-113423400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr2:113411200-113428200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:113411400-113423400	Strong transcription	Fetal Stomach	stomach
35	chr2:113412600-113423200	Strong transcription	Rectal Smooth Muscle	rectum
36	chr2:113412600-113423400	Strong transcription	Thymus	Thymus
37	chr2:113412800-113423400	Strong transcription	NHLF	lung
38	chr2:113414000-113422800	Strong transcription	Brain Cingulate Gyrus	brain
39	chr2:113414000-113423600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:113414200-113423400	Genic enhancers	K562	blood
41	chr2:113414400-113422400	Strong transcription	Brain Hippocampus Middle	brain
42	chr2:113414400-113423000	Strong transcription	Fetal Brain Female	brain
43	chr2:113414800-113422800	Strong transcription	Placenta	Placenta
44	chr2:113415400-113422200	Strong transcription	Left Ventricle	heart
45	chr2:113415600-113423200	Strong transcription	Brain Germinal Matrix	brain
46	chr2:113415800-113423400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:113415800-113423600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:113416000-113423400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:113416800-113423200	Strong transcription	NH-A	brain
50	chr2:113417200-113423000	Strong transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links