Variant report

Variant	rs2627817
Chromosome Location	chr4:143190816-143190817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10029437	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1219266	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs1219268	1.00[CEU][hapmap]
rs1219269	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs1219270	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs1390994	1.00[CEU][hapmap]
rs1497139	1.00[CEU][hapmap]
rs1532450	1.00[CEU][hapmap]
rs1907109	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907117	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1907119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1907135	1.00[CEU][hapmap]
rs1907137	0.87[CEU][hapmap]
rs1948323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2130685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2172023	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627812	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627816	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2627834	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627835	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627836	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636635	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2636637	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs2636641	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636642	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636643	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636647	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636652	1.00[CHD][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs2636655	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636656	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636657	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636660	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636679	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2636685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102436	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3102437	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3102439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102443	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3102444	0.96[EUR][1000 genomes]
rs3102446	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113511	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113513	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113515	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113522	0.87[CEU][hapmap]
rs336384	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs336393	0.81[TSI][hapmap]
rs336394	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs336400	0.81[CEU][hapmap]
rs336402	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs336405	0.81[CEU][hapmap]
rs336406	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs336408	0.88[TSI][hapmap]
rs34648309	0.82[EUR][1000 genomes]
rs992257	0.85[TSI][hapmap]

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	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	nsv830098	chr4:143050143-143234384	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv595604	chr4:143077401-143228914	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143179800-143191000	Weak transcription	Colonic Mucosa	Colon
2	chr4:143181400-143191400	Weak transcription	Left Ventricle	heart
3	chr4:143181600-143195600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:143183000-143204800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:143185400-143192400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:143185400-143199000	Weak transcription	Psoas Muscle	Psoas
7	chr4:143186400-143191200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:143186600-143191200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:143186600-143199800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:143187400-143191200	Weak transcription	Dnd41	blood
11	chr4:143187400-143193000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:143187400-143193600	Weak transcription	Small Intestine	intestine
13	chr4:143187400-143197200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:143187400-143199400	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:143187400-143199400	Weak transcription	NH-A	brain
16	chr4:143187400-143200400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:143187400-143203800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:143187400-143218600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:143187600-143192600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:143187600-143194600	Weak transcription	NHLF	lung
21	chr4:143187600-143196000	Weak transcription	A549	lung
22	chr4:143187600-143200600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:143187800-143194000	Weak transcription	NHEK	skin
24	chr4:143188800-143191200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr4:143188800-143191400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:143188800-143194000	Weak transcription	NHDF-Ad	bronchial
27	chr4:143189000-143193000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:143189600-143191200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:143189600-143192200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr4:143189600-143192200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:143189600-143192800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr4:143189800-143191800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr4:143189800-143191800	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr4:143190000-143191200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:143190000-143191400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:143190000-143191800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr4:143190000-143191800	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr4:143190000-143192000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:143190000-143192000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:143190000-143192000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:143190000-143192800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:143190200-143191400	Strong transcription	HSMMtube	muscle
43	chr4:143190200-143191600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr4:143190200-143191600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr4:143190200-143191600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr4:143190200-143191800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:143190200-143192200	Strong transcription	Primary T cells from cord blood	blood
48	chr4:143190200-143192800	Strong transcription	HMEC	breast
49	chr4:143190400-143191600	Strong transcription	HSMM	muscle
50	chr4:143190400-143191800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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