Variant report

Variant	rs749454
Chromosome Location	chr2:33502003-33502004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33169785..33172664-chr2:33500827..33503324,2	K562	blood:

Variant related genes	Relation type
ENSG00000206951	Chromatin interaction
ENSG00000049323	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10169788	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs10175557	0.87[ASN][1000 genomes]
rs10175619	0.83[ASN][1000 genomes]
rs11124313	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11673950	0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs11684829	0.87[ASN][1000 genomes]
rs13391131	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs13392154	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs13394195	0.83[ASN][1000 genomes]
rs13414720	0.82[ASN][1000 genomes]
rs17582516	0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2603361	0.91[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs3769540	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs3769545	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4233909	0.87[ASN][1000 genomes]
rs4670387	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4670408	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs62148881	0.91[ASN][1000 genomes]
rs62148882	0.91[ASN][1000 genomes]
rs62148931	0.83[ASN][1000 genomes]
rs6543704	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6543705	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6711027	0.87[ASN][1000 genomes]
rs6739030	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs6739506	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6739725	0.87[ASN][1000 genomes]
rs6742198	0.85[JPT][hapmap]
rs6751758	1.00[JPT][hapmap]
rs711234	0.91[CHB][hapmap]
rs711235	0.91[CHB][hapmap]
rs723043	0.83[ASN][1000 genomes]
rs7565095	0.87[ASN][1000 genomes]
rs7581438	0.81[ASN][1000 genomes]
rs7586227	0.86[ASN][1000 genomes]
rs7590205	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs817529	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs817532	0.90[CHB][hapmap];0.89[ASN][1000 genomes]
rs817534	1.00[CHB][hapmap]
rs817536	0.91[CHB][hapmap]
rs817537	0.91[CHB][hapmap]
rs817539	0.85[ASN][1000 genomes]
rs9308934	0.88[JPT][hapmap]
rs971793	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][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	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33472000-33516600	Weak transcription	Psoas Muscle	Psoas
2	chr2:33487000-33509800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:33487800-33502400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:33490600-33515600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:33491800-33504400	Weak transcription	Colonic Mucosa	Colon
6	chr2:33492000-33515800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:33492200-33516600	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:33492200-33516600	Weak transcription	Brain Substantia Nigra	brain
9	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
10	chr2:33492600-33508400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:33493600-33515200	Weak transcription	Fetal Lung	lung
12	chr2:33493800-33503400	Weak transcription	Fetal Brain Female	brain
13	chr2:33493800-33515400	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:33494200-33506200	Weak transcription	Fetal Heart	heart
15	chr2:33494200-33516000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:33494200-33516200	Weak transcription	Fetal Kidney	kidney
17	chr2:33494600-33515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:33497800-33503400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:33499200-33508000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:33499400-33502400	Strong transcription	Liver	Liver
21	chr2:33499600-33502200	Strong transcription	Aorta	Aorta
22	chr2:33499800-33502400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:33500000-33502200	Strong transcription	Fetal Stomach	stomach
24	chr2:33500000-33502400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:33500200-33504800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:33500400-33502400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:33500400-33502600	Genic enhancers	Muscle Satellite Cultured Cells	--
28	chr2:33500800-33502400	Enhancers	Esophagus	oesophagus
29	chr2:33500800-33502400	Genic enhancers	Osteobl	bone
30	chr2:33500800-33502600	Genic enhancers	Fetal Muscle Leg	muscle
31	chr2:33500800-33503800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
32	chr2:33501000-33502400	Strong transcription	Placenta	Placenta
33	chr2:33501000-33502600	Strong transcription	Right Ventricle	heart
34	chr2:33501000-33503200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:33501000-33503200	Weak transcription	Gastric	stomach
36	chr2:33501000-33503200	Weak transcription	HMEC	breast
37	chr2:33501200-33502200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:33501200-33502600	Genic enhancers	Stomach Smooth Muscle	stomach
39	chr2:33501200-33505400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:33501200-33505600	Weak transcription	NHLF	lung
41	chr2:33501200-33511000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:33501200-33516400	Weak transcription	Stomach Mucosa	stomach
43	chr2:33501200-33528800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:33501400-33502400	Enhancers	Pancreas	Pancrea
45	chr2:33501400-33502800	Enhancers	A549	lung
46	chr2:33501400-33503400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:33501400-33503600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:33501400-33503600	Weak transcription	HSMM	muscle
49	chr2:33501400-33516600	Weak transcription	K562	blood
50	chr2:33501600-33502200	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links