Variant report

Variant	rs4670408
Chromosome Location	chr2:33516152-33516153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr2:33516028-33517105	A549	lung:	n/a	n/a
2	SP1	chr2:33516089-33517253	A549	lung:	n/a	n/a
3	NFIC	chr2:33516133-33517040	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr2:33515710-33517267	A549	lung:	n/a	n/a
5	GATA3	chr2:33516143-33517122	A549	lung:	n/a	chr2:33517012-33517022
6	SP1	chr2:33516131-33517212	A549	lung:	n/a	n/a
7	GATA3	chr2:33516028-33517006	SK-N-SH	brain:	n/a	n/a
8	STAT3	chr2:33515962-33516174	MCF10A-Er-Src	breast:	n/a	n/a
9	FOXA2	chr2:33516083-33516924	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:33516131-33516966	PFSK-1	brain:	n/a	n/a
11	GATA3	chr2:33516149-33516955	SK-N-SH	brain:	n/a	n/a
12	BCL3	chr2:33516117-33516981	A549	lung:	n/a	n/a
13	PBX3	chr2:33516108-33516896	SK-N-SH	brain:	n/a	n/a
14	FOXA2	chr2:33516055-33517054	A549	lung:	n/a	n/a
15	EP300	chr2:33516060-33517152	A549	lung:	n/a	chr2:33517010-33517024
16	REST	chr2:33516090-33517054	A549	lung:	n/a	n/a
17	TCF12	chr2:33516105-33517099	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LTBP1	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10169788	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10175557	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175619	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11124313	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11673950	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11684829	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13392154	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13394170	0.83[ASN][1000 genomes]
rs13394195	0.96[CEU][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13403065	0.84[CEU][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs13414720	0.87[ASN][1000 genomes]
rs17582516	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2603361	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3769540	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769542	0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs3769544	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3769545	0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs41464348	0.83[MEX][hapmap]
rs4233909	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4670387	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62148881	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62148882	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62148927	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62148931	0.81[ASN][1000 genomes]
rs6543704	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543705	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6711027	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6739030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739506	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6739725	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6751758	0.86[JPT][hapmap]
rs711234	0.91[CHB][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs711235	0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes]
rs723043	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs749454	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7565095	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575377	0.83[MEX][hapmap]
rs7581438	0.86[ASN][1000 genomes]
rs7586227	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7590205	0.80[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7605474	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs817529	0.80[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs817532	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs817534	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs817535	0.83[MEX][hapmap]
rs817536	0.80[ASW][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs817537	0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs817539	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9308934	0.84[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs971793	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1011020	chr2:33508811-33527784	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33472000-33516600	Weak transcription	Psoas Muscle	Psoas
2	chr2:33492200-33516600	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:33492200-33516600	Weak transcription	Brain Substantia Nigra	brain
4	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
5	chr2:33494200-33516200	Weak transcription	Fetal Kidney	kidney
6	chr2:33501200-33516400	Weak transcription	Stomach Mucosa	stomach
7	chr2:33501200-33528800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:33501400-33516600	Weak transcription	K562	blood
9	chr2:33501800-33517800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:33502400-33516600	Weak transcription	Pancreas	Pancrea
11	chr2:33502400-33516600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:33502400-33516800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:33502400-33516800	Weak transcription	Esophagus	oesophagus
14	chr2:33502600-33537000	Weak transcription	Fetal Intestine Large	intestine
15	chr2:33503600-33518200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:33505000-33526200	Weak transcription	Placenta	Placenta
17	chr2:33507000-33528600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:33513600-33516600	Weak transcription	Left Ventricle	heart
19	chr2:33514600-33516400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:33514800-33516600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:33515000-33516200	Enhancers	Ovary	ovary
22	chr2:33515000-33516400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:33515200-33516200	Enhancers	NH-A	brain
24	chr2:33515200-33516400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:33515200-33516400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr2:33515200-33516400	Enhancers	NHLF	lung
27	chr2:33515200-33516600	Enhancers	Fetal Lung	lung
28	chr2:33515200-33516600	Enhancers	HSMMtube	muscle
29	chr2:33515200-33517000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:33515200-33517000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr2:33515200-33517000	Enhancers	Fetal Stomach	stomach
32	chr2:33515200-33519200	Enhancers	Fetal Heart	heart
33	chr2:33515400-33516400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:33515400-33516400	Enhancers	NHDF-Ad	bronchial
35	chr2:33515400-33516400	Enhancers	Osteobl	bone
36	chr2:33515400-33516600	Enhancers	Colon Smooth Muscle	Colon
37	chr2:33515400-33517000	Enhancers	Fetal Muscle Leg	muscle
38	chr2:33515600-33516200	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr2:33515600-33516400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:33515600-33516600	Enhancers	Liver	Liver
41	chr2:33515600-33516600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr2:33515600-33516600	Weak transcription	Small Intestine	intestine
43	chr2:33515800-33516200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:33515800-33516600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:33515800-33516600	Weak transcription	Aorta	Aorta
46	chr2:33515800-33516600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr2:33515800-33516600	Enhancers	Hela-S3	cervix
48	chr2:33515800-33516600	Enhancers	HSMM	muscle
49	chr2:33515800-33517000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:33515800-33517200	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links