Variant report

Variant	rs3113246
Chromosome Location	chr4:107204538-107204539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10004034	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10025668	0.83[ASN][1000 genomes]
rs10516530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10516531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097923	1.00[ASN][1000 genomes]
rs1134648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11938792	1.00[ASN][1000 genomes]
rs12508029	0.96[ASN][1000 genomes]
rs12512475	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17036581	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2212969	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2691805	0.95[ASN][1000 genomes]
rs2691806	0.95[ASN][1000 genomes]
rs2728176	0.95[ASN][1000 genomes]
rs2728177	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28418378	0.83[ASN][1000 genomes]
rs28600991	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2949626	0.94[ASN][1000 genomes]
rs2949649	0.88[ASN][1000 genomes]
rs2949651	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3018057	0.88[ASN][1000 genomes]
rs3018059	0.94[ASN][1000 genomes]
rs3018067	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3109950	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3109951	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3109952	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3109954	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3109956	0.95[ASN][1000 genomes]
rs3109959	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3113251	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3133167	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3133172	0.95[ASN][1000 genomes]
rs3133173	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs34305991	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34909190	0.91[ASN][1000 genomes]
rs34923623	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4415033	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4441824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4516801	1.00[CEU][hapmap]
rs4533833	0.91[ASN][1000 genomes]
rs4560491	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4582218	0.99[ASN][1000 genomes]
rs57983950	0.99[ASN][1000 genomes]
rs6533241	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836796	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6848855	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7442226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669347	0.84[ASN][1000 genomes]
rs7677394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7680756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7694217	1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs9884121	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9991203	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs9993259	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879704	chr4:107095901-107212966	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879705	chr4:107179126-107212966	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv830029	chr4:107203096-107353483	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107114600-107236000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:107141600-107214800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:107155600-107236000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr4:107170800-107208200	Weak transcription	Fetal Kidney	kidney
5	chr4:107177400-107207600	Weak transcription	Fetal Brain Female	brain
6	chr4:107177600-107205600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:107177800-107207600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:107177800-107207600	Weak transcription	Adipose Nuclei	Adipose
9	chr4:107177800-107211600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:107177800-107215200	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:107178000-107205400	Weak transcription	Thymus	Thymus
12	chr4:107178000-107207800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr4:107178000-107207800	Weak transcription	Lung	lung
14	chr4:107178000-107207800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:107178000-107208200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:107178000-107208400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:107178000-107211800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:107178000-107211800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:107178000-107211800	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:107178000-107211800	Weak transcription	Fetal Stomach	stomach
21	chr4:107178000-107211800	Weak transcription	Left Ventricle	heart
22	chr4:107178000-107211800	Weak transcription	Ovary	ovary
23	chr4:107178000-107236200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:107178000-107236200	Weak transcription	Right Ventricle	heart
25	chr4:107178000-107236600	Weak transcription	Esophagus	oesophagus
26	chr4:107178000-107236600	Weak transcription	Pancreas	Pancrea
27	chr4:107178200-107211600	Weak transcription	Placenta	Placenta
28	chr4:107178200-107236000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:107179000-107211400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr4:107179800-107208600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:107180600-107207000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:107180600-107207400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:107186000-107211800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:107186200-107207600	Weak transcription	Liver	Liver
35	chr4:107186200-107207800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr4:107186200-107212800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:107187000-107208200	Weak transcription	Fetal Intestine Large	intestine
38	chr4:107187600-107215200	Weak transcription	Fetal Intestine Small	intestine
39	chr4:107190800-107208600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:107192000-107208600	Weak transcription	HSMMtube	muscle
41	chr4:107192400-107215200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:107192600-107208000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:107194000-107207600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:107194200-107211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:107194400-107221200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:107194800-107227600	Weak transcription	Brain Angular Gyrus	brain
47	chr4:107195000-107207800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:107195000-107208600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:107195200-107206800	Weak transcription	GM12878-XiMat	blood
50	chr4:107195400-107213000	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links