Variant report

Variant	rs4663089
Chromosome Location	chr2:127809508-127809509
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11888878	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11893989	0.86[EUR][1000 genomes]
rs11902275	0.85[EUR][1000 genomes]
rs12465042	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12474412	0.87[EUR][1000 genomes]
rs12476339	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12477924	0.87[EUR][1000 genomes]
rs17014784	0.86[EUR][1000 genomes]
rs17014818	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17014851	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs17040070	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2071268	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs2071270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3768859	1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[EUR][1000 genomes]
rs3768860	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4662703	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4663090	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55819047	0.86[EUR][1000 genomes]
rs55999604	0.86[EUR][1000 genomes]
rs56408880	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60022219	0.86[EUR][1000 genomes]
rs66507470	0.81[EUR][1000 genomes]
rs6745677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67920725	0.86[EUR][1000 genomes]
rs72481904	0.92[EUR][1000 genomes]
rs727095	0.86[EUR][1000 genomes]
rs72846676	0.92[EUR][1000 genomes]
rs7570116	0.83[EUR][1000 genomes]
rs7573824	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs880436	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv459230	chr2:127771006-127844735	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv583032	chr2:127771006-127844735	Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1003730	chr2:127794288-127860830	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1003461	chr2:127794288-127862257	Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv516759	chr2:127796666-127859441	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1000994	chr2:127797089-127860830	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv1825024	chr2:127798138-127864285	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv459241	chr2:127800981-127868435	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv583033	chr2:127800981-127868435	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv875011	chr2:127800981-127868435	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv875012	chr2:127800981-127895573	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1002673	chr2:127801964-127860830	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1010577	chr2:127801964-127862257	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1011224	chr2:127802375-127860830	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv1003887	chr2:127802375-127862257	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1009309	chr2:127802730-127862257	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv1014290	chr2:127805366-127860830	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv1010084	chr2:127805366-127862257	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv997855	chr2:127806424-127857946	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	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127783800-127815600	Weak transcription	Aorta	Aorta
2	chr2:127798200-127811400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:127802000-127818800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:127802200-127813600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:127802400-127816000	Weak transcription	Fetal Brain Male	brain
6	chr2:127802400-127822800	Weak transcription	Fetal Kidney	kidney
7	chr2:127803800-127814200	Weak transcription	HSMM	muscle
8	chr2:127804000-127810600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:127804000-127813400	Weak transcription	Primary B cells from cord blood	blood
10	chr2:127804000-127814400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:127804200-127818200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:127804200-127819600	Weak transcription	Osteobl	bone
13	chr2:127804400-127820000	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr2:127804600-127810000	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr2:127804600-127811400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:127804600-127817400	Genic enhancers	Fetal Muscle Leg	muscle
17	chr2:127804600-127819200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:127804800-127818200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:127804800-127819400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:127805200-127811200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:127805400-127822200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:127805800-127822200	Weak transcription	Small Intestine	intestine
23	chr2:127806400-127811600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:127806400-127814200	Weak transcription	Ovary	ovary
25	chr2:127806400-127821800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:127806600-127810800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:127806600-127812600	Genic enhancers	Brain Hippocampus Middle	brain
28	chr2:127806800-127810600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:127806800-127819000	Weak transcription	Right Atrium	heart
30	chr2:127807000-127810800	Weak transcription	Liver	Liver
31	chr2:127807000-127812000	Genic enhancers	Brain Cingulate Gyrus	brain
32	chr2:127807000-127813400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:127807000-127818800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:127807200-127810800	Weak transcription	Fetal Intestine Large	intestine
35	chr2:127807200-127812600	Genic enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:127807200-127817200	Weak transcription	Fetal Thymus	thymus
37	chr2:127807400-127809600	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr2:127807400-127810200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:127807400-127813800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:127807400-127814000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:127807400-127821800	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:127807600-127812200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:127807800-127810600	Weak transcription	A549	lung
44	chr2:127807800-127811000	Strong transcription	Fetal Intestine Small	intestine
45	chr2:127807800-127811400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr2:127807800-127811600	Weak transcription	Fetal Lung	lung
47	chr2:127807800-127813600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:127807800-127820000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:127807800-127820800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:127807800-127821600	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links