Variant report

Variant	rs742099
Chromosome Location	chr6:15496662-15496663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:15496588-15496765	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF3	chr6:15496394-15496794	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:15496114-15498485	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:15494778-15497166	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:15496615-15496665	AoSMC	blood vessel:	n/a
2	chr6:15496615-15496665	NHDF-neo	bronchial:	n/a
3	chr6:15496615-15496665	GM06990	blood:	n/a
4	chr6:15496615-15496665	RPTEC	kidney:	n/a
5	chr6:15496615-15496665	HCM	heart:	n/a
6	chr6:15496615-15496665	CMK	blood:	n/a
7	chr6:15496615-15496665	HIPEpiC	eye:	n/a
8	chr6:15496615-15496665	GM12891	blood:	n/a
9	chr6:15496615-15496665	HEEpiC	esophagus:	n/a
10	chr6:15496615-15496665	HUVEC	blood vessel:	n/a
11	chr6:15496615-15496665	NHBE	bronchial:	n/a
12	chr6:15496615-15496665	HL-60	blood:	n/a
13	chr6:15496615-15496665	HNPCEpiC	eye:	n/a
14	chr6:15496615-15496665	T-47D	breast:	n/a
15	chr6:15496615-15496665	K562	blood:	n/a
16	chr6:15496615-15496665	Hepatocyte	liver:	n/a
17	chr6:15496615-15496665	Caco-2	colon:	n/a
18	chr6:15496615-15496665	SK-N-SH_RA	brain:	n/a
19	chr6:15496615-15496665	HRPEpiC	eye:	n/a
20	chr6:15496615-15496665	HPAEpiC	pulmonary alveolar:	n/a
21	chr6:15496615-15496665	SK-N-MC	brain:	n/a
22	chr6:15496615-15496665	PFSK-1	brain:	n/a
23	chr6:15496615-15496665	BJ	skin:	n/a
24	chr6:15496615-15496665	NH-A	brain:	n/a
25	chr6:15496615-15496665	HRE	kidney:	n/a
26	chr6:15496615-15496665	MCF-7	breast:	n/a
27	chr6:15496615-15496665	NT2-D1	testis:	n/a
28	chr6:15496615-15496665	U87	brain:	n/a
29	chr6:15496615-15496665	HCPEpiC	choroid plexus:	n/a
30	chr6:15496615-15496665	ECC-1	luminal epithelium:	n/a
31	chr6:15496615-15496665	PrEC	prostate:	n/a
32	chr6:15496615-15496665	PANC-1	pancreas:	n/a
33	chr6:15496615-15496665	ProgFib	skin:	n/a
34	chr6:15496615-15496665	Jurkat	blood:	n/a
35	chr6:15496615-15496665	ovcar-3	ovarian:	n/a
36	chr6:15496615-15496665	GM19239	blood:	n/a
37	chr6:15496615-15496665	AG04449	skin:	fetal
38	chr6:15496615-15496665	HepG2	liver:	n/a
39	chr6:15496615-15496665	HEK293	kidney:	embryo
40	chr6:15496615-15496665	LNCaP	prostate:	n/a
41	chr6:15496615-15496665	SAEC	small airway:	n/a
42	chr6:15496615-15496665	AG09319	gingival:	n/a
43	chr6:15496615-15496665	GM12892	blood:	n/a
44	chr6:15496615-15496665	SK-N-SH	brain:	n/a
45	chr6:15496615-15496665	GM12878	blood:	n/a
46	chr6:15496615-15496665	AG09309	skin:	n/a
47	chr6:15496615-15496665	HAEpiC	amniotic membrane:	n/a
48	chr6:15496615-15496665	Hela-S3	cervix:	n/a
49	chr6:15496615-15496665	IMR90	lung:	fetal
50	chr6:15496615-15496665	MCF10A-Er-Src	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15494495..15496719-chr6:15502901..15504506,2	K562	blood:
2	chr6:15211347..15213015-chr6:15495121..15498048,2	K562	blood:

No data

Variant related genes	Relation type
JARID2	TF binding region
JARID2	CpG island

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10949304	0.92[ASN][1000 genomes]
rs11964846	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11966626	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13192234	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13192892	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13194650	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13196869	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13198780	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13202100	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13202955	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13204842	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13208563	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13209668	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17455404	0.82[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs1967664	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076056	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237138	0.88[EUR][1000 genomes]
rs2299043	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs35868206	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3819396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712251	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs4715975	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715979	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4715980	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6899342	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6899343	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6917591	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs742100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7756331	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7761778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769291	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7774429	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383056	0.87[EUR][1000 genomes]
rs9383062	0.93[EUR][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	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv522265	chr6:15494177-15546213	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15471000-15502000	Weak transcription	A549	lung
2	chr6:15486800-15502000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:15487200-15508000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr6:15489200-15496800	Weak transcription	Colonic Mucosa	Colon
5	chr6:15489200-15504400	Weak transcription	Fetal Brain Female	brain
6	chr6:15490800-15496800	Enhancers	HSMMtube	muscle
7	chr6:15491800-15501400	Weak transcription	NH-A	brain
8	chr6:15492000-15496800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:15492000-15498400	Weak transcription	Stomach Mucosa	stomach
10	chr6:15492000-15501800	Weak transcription	Fetal Brain Male	brain
11	chr6:15492200-15501200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:15492200-15507800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:15492200-15508200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr6:15492200-15527000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:15492400-15498600	Weak transcription	Brain Substantia Nigra	brain
16	chr6:15492400-15502400	Strong transcription	Fetal Intestine Small	intestine
17	chr6:15492400-15527200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:15492600-15522200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:15492800-15515000	Strong transcription	Thymus	Thymus
20	chr6:15492800-15527000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:15493000-15501600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:15493000-15501600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:15493000-15501800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:15493000-15504200	Strong transcription	Fetal Thymus	thymus
25	chr6:15493400-15502000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr6:15493800-15497000	Weak transcription	GM12878-XiMat	blood
27	chr6:15493800-15520000	Weak transcription	Hela-S3	cervix
28	chr6:15494200-15522400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr6:15494400-15498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:15494400-15501600	Weak transcription	Fetal Kidney	kidney
31	chr6:15494600-15506000	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:15494600-15507400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:15494800-15524000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:15494800-15527000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr6:15495000-15499200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:15495000-15499800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:15495000-15527200	Strong transcription	Dnd41	blood
38	chr6:15495000-15529200	Strong transcription	Primary T cells from cord blood	blood
39	chr6:15495200-15508400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:15495200-15525800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:15495400-15497600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:15495400-15497600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr6:15495400-15498400	Strong transcription	NHEK	skin
44	chr6:15495400-15498600	Strong transcription	Spleen	Spleen
45	chr6:15495400-15504200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:15495400-15504800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:15495400-15506400	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr6:15495400-15508600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr6:15495400-15525000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:15495600-15496800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links