Variant report

Variant	rs3829747
Chromosome Location	chr2:179397561-179397562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:179397513-179397563	GM19239	blood:	n/a
2	chr2:179397513-179397563	HCPEpiC	choroid plexus:	n/a
3	chr2:179397513-179397563	NHDF-neo	bronchial:	n/a
4	chr2:179397513-179397563	MCF10A-Er-Src	breast:	n/a
5	chr2:179397513-179397563	IMR90	lung:	fetal
6	chr2:179397513-179397563	HPAEpiC	pulmonary alveolar:	n/a
7	chr2:179397513-179397563	ECC-1	luminal epithelium:	n/a
8	chr2:179397513-179397563	PFSK-1	brain:	n/a
9	chr2:179397513-179397563	Caco-2	colon:	n/a
10	chr2:179397513-179397563	Hepatocyte	liver:	n/a
11	chr2:179397513-179397563	Jurkat	blood:	n/a
12	chr2:179397513-179397563	ovcar-3	ovarian:	n/a
13	chr2:179397513-179397563	SK-N-SH_RA	brain:	n/a
14	chr2:179397513-179397563	T-47D	breast:	n/a
15	chr2:179397513-179397563	GM12891	blood:	n/a
16	chr2:179397513-179397563	BJ	skin:	n/a
17	chr2:179397513-179397563	GM12878	blood:	n/a
18	chr2:179397513-179397563	H1-hESC	embryonic stem cell:	embryo
19	chr2:179397513-179397563	U87	brain:	n/a
20	chr2:179397513-179397563	RPTEC	kidney:	n/a
21	chr2:179397513-179397563	SK-N-SH	brain:	n/a
22	chr2:179397513-179397563	HCT-116	colon:	n/a
23	chr2:179397513-179397563	NHBE	bronchial:	n/a
24	chr2:179397513-179397563	HepG2	liver:	n/a
25	chr2:179397513-179397563	HRE	kidney:	n/a
26	chr2:179397513-179397563	HNPCEpiC	eye:	n/a
27	chr2:179397513-179397563	CMK	blood:	n/a
28	chr2:179397513-179397563	AG04449	skin:	fetal
29	chr2:179397513-179397563	MCF-7	breast:	n/a
30	chr2:179397513-179397563	HEK293	kidney:	embryo
31	chr2:179397513-179397563	K562	blood:	n/a
32	chr2:179397513-179397563	SKMC	muscle:	n/a
33	chr2:179397513-179397563	HMEC	breast:	n/a
34	chr2:179397513-179397563	HEEpiC	esophagus:	n/a
35	chr2:179397513-179397563	PANC-1	pancreas:	n/a
36	chr2:179397513-179397563	HRPEpiC	eye:	n/a
37	chr2:179397513-179397563	GM06990	blood:	n/a
38	chr2:179397513-179397563	HIPEpiC	eye:	n/a
39	chr2:179397513-179397563	AG09319	gingival:	n/a
40	chr2:179397513-179397563	AG09309	skin:	n/a
41	chr2:179397513-179397563	AG04450	lung:	fetal
42	chr2:179397513-179397563	HL-60	blood:	n/a
43	chr2:179397513-179397563	SK-N-MC	brain:	n/a
44	chr2:179397513-179397563	HUVEC	blood vessel:	n/a
45	chr2:179397513-179397563	BE2_C	brain:	n/a
46	chr2:179397513-179397563	AG10803	skin:	n/a
47	chr2:179397513-179397563	NB4	blood:	n/a
48	chr2:179397513-179397563	HCM	heart:	n/a
49	chr2:179397513-179397563	LNCaP	prostate:	n/a
50	chr2:179397513-179397563	NH-A	brain:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:179395497..179400266-chr2:179412543..179417721,4	K562	blood:
2	chr2:179395770..179398427-chr2:179417927..179420746,2	K562	blood:
3	chr2:179386919..179391089-chr2:179391647..179398872,11	K562	blood:

No data

Variant related genes	Relation type
TTN-AS1	CpG island
ENSG00000237298	Chromatin interaction
ENSG00000270277	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1007025	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12614435	0.91[CEU][hapmap];0.89[GIH][hapmap]
rs12618265	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12998857	0.91[CEU][hapmap]
rs13005601	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13009158	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13029629	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13034990	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16866358	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16866365	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16866369	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16866373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866397	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16866406	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16866457	0.82[YRI][hapmap]
rs16866467	0.82[YRI][hapmap]
rs16866475	0.82[YRI][hapmap]
rs2288325	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288569	1.00[ASW][hapmap];0.83[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288571	0.91[CEU][hapmap]
rs2303539	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303828	0.89[GIH][hapmap]
rs2303838	0.85[GIH][hapmap]
rs2857265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731746	0.83[CEU][hapmap];0.87[GIH][hapmap]
rs3731748	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731749	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755456	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs744426	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7597154	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs890578	0.91[CEU][hapmap];0.87[GIH][hapmap]

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	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv522036	chr2:179395760-179398509	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179403600	Weak transcription	Esophagus	oesophagus
2	chr2:179388800-179408000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:179388800-179408600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:179388800-179410600	Weak transcription	Colonic Mucosa	Colon
5	chr2:179388800-179411800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:179388800-179417600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:179388800-179429400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:179388800-179441800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:179388800-179448800	Weak transcription	Small Intestine	intestine
10	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:179389200-179412600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:179389400-179397800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:179389400-179397800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:179389400-179398800	Weak transcription	HUVEC	blood vessel
15	chr2:179389400-179399000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:179389400-179401600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:179389400-179404000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:179389400-179404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:179389400-179405800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:179389400-179408200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:179389400-179408800	Weak transcription	HMEC	breast
22	chr2:179389400-179410000	Weak transcription	Hela-S3	cervix
23	chr2:179389400-179412800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:179389400-179413000	Weak transcription	Fetal Brain Male	brain
25	chr2:179389400-179413400	Weak transcription	NH-A	brain
26	chr2:179389400-179416800	Weak transcription	Stomach Mucosa	stomach
27	chr2:179389400-179417200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:179389400-179417200	Weak transcription	NHDF-Ad	bronchial
29	chr2:179389400-179417200	Weak transcription	NHLF	lung
30	chr2:179389400-179428200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:179389600-179397600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:179390600-179426400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:179391200-179419200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:179393600-179398800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:179393800-179439800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:179394800-179412600	Strong transcription	Primary T cells from cord blood	blood
37	chr2:179394800-179413400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:179394800-179417600	Strong transcription	HSMMtube	muscle
39	chr2:179394800-179421600	Strong transcription	Left Ventricle	heart
40	chr2:179395400-179401000	Strong transcription	Fetal Stomach	stomach
41	chr2:179395400-179414200	Strong transcription	Fetal Thymus	thymus
42	chr2:179395400-179423000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:179395600-179398400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:179395600-179398400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:179395600-179400600	Strong transcription	Fetal Intestine Small	intestine
46	chr2:179395600-179414200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:179395600-179421600	Strong transcription	Fetal Heart	heart
48	chr2:179395800-179398200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:179395800-179399400	Strong transcription	K562	blood
50	chr2:179395800-179399800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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