Variant report

Variant	rs2636671
Chromosome Location	chr4:143234955-143234956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1817971	0.80[ASN][1000 genomes]
rs2627802	1.00[ASW][hapmap];0.89[MKK][hapmap];0.81[EUR][1000 genomes]
rs2627814	0.85[EUR][1000 genomes]
rs2635425	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2635426	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2635427	0.82[EUR][1000 genomes]
rs2635428	0.86[EUR][1000 genomes]
rs2635429	0.95[GIH][hapmap]
rs2636639	0.82[CEU][hapmap]
rs2636670	0.95[CHD][hapmap];0.83[GIH][hapmap];0.82[ASN][1000 genomes]
rs2646096	0.85[EUR][1000 genomes]
rs6844681	0.92[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.88[EUR][1000 genomes]
rs960679	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2636671	ABCE1	cis	cerebellum	SCAN
rs2636671	C4orf49	cis	cerebellum	SCAN
rs2636671	NDUFC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143200000-143240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:143210800-143235400	Weak transcription	Right Ventricle	heart
3	chr4:143215200-143235200	Weak transcription	Osteobl	bone
4	chr4:143215800-143235200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:143217600-143238600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:143217600-143260800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:143219400-143236600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:143223600-143239200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:143225200-143235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:143225400-143237400	Weak transcription	Ovary	ovary
11	chr4:143225400-143240200	Weak transcription	Esophagus	oesophagus
12	chr4:143229000-143235600	Strong transcription	NHEK	skin
13	chr4:143229400-143235600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:143231000-143235000	Weak transcription	Fetal Intestine Small	intestine
15	chr4:143231200-143235400	Weak transcription	Gastric	stomach
16	chr4:143231200-143235400	Weak transcription	Psoas Muscle	Psoas
17	chr4:143231400-143239400	Weak transcription	HSMMtube	muscle
18	chr4:143231800-143235400	Strong transcription	HSMM	muscle
19	chr4:143232000-143236200	Strong transcription	HMEC	breast
20	chr4:143232200-143235000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:143232400-143235200	Weak transcription	Fetal Stomach	stomach
22	chr4:143232400-143236200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:143232600-143235400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:143232800-143236200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:143233000-143236200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr4:143233200-143235400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr4:143233400-143235000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr4:143233600-143235000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr4:143233600-143236200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:143233800-143235200	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr4:143233800-143236200	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr4:143233800-143241000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr4:143233800-143257200	Weak transcription	Left Ventricle	heart
34	chr4:143234000-143235000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:143234000-143235600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:143234000-143236000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr4:143234000-143236000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:143234000-143236200	Enhancers	Fetal Thymus	thymus
39	chr4:143234000-143236400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:143234000-143242000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:143234200-143235800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr4:143234200-143236000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr4:143234200-143240000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:143234400-143235000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:143234400-143235200	Enhancers	Colonic Mucosa	Colon
46	chr4:143234400-143235400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:143234400-143235600	Enhancers	Fetal Intestine Large	intestine
48	chr4:143234400-143236200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:143234600-143235000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:143234600-143235000	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links