Variant report

Variant	rs11498195
Chromosome Location	chr6:45390949-45390950
allele	C/G
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	ZBTB7A	chr6:45390219-45391659	ECC-1	luminal epithelium:	n/a	chr6:45391071-45391078
2	CHD2	chr6:45390938-45390992	GM12878	blood:	n/a	n/a
3	EP300	chr6:45389200-45391505	SK-N-SH	brain:	n/a	n/a
4	HDAC2	chr6:45390827-45391509	MCF-7	breast:	n/a	n/a
5	ELF1	chr6:45390635-45390964	GM12878	blood:	n/a	n/a
6	SP4	chr6:45390887-45391107	H1-hESC	embryonic stem cell:	n/a	chr6:45391066-45391082 chr6:45391064-45391080
7	ZBTB7A	chr6:45390400-45391623	ECC-1	luminal epithelium:	n/a	chr6:45391071-45391078
8	EBF1	chr6:45390929-45391244	GM12878	blood:	n/a	chr6:45391105-45391115 chr6:45391104-45391115 chr6:45391106-45391115 chr6:45391104-45391117
9	MAX	chr6:45389313-45391254	NB4	blood:	n/a	n/a
10	RAD21	chr6:45388419-45392074	IMR90	lung:	n/a	chr6:45391794-45391808 chr6:45392039-45392052 chr6:45390904-45390916 chr6:45390740-45390753 chr6:45391581-45391591 chr6:45388466-45388478
11	POLR2A	chr6:45390397-45391257	ProgFib	skin:	n/a	n/a
12	POLR2A	chr6:45389182-45392710	HL-60	blood:	n/a	n/a
13	E2F6	chr6:45390810-45391355	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr6:45389166-45392571	HL-60	blood:	n/a	n/a
15	CHD1	chr6:45388363-45391883	IMR90	lung:	n/a	chr6:45391066-45391076 chr6:45391635-45391645
16	ZNF263	chr6:45390603-45391393	HEK293-T-REx	kidney:	n/a	n/a
17	SIN3AK20	chr6:45390908-45391555	PANC-1	pancreas:	n/a	n/a
18	ZNF143	chr6:45390066-45391433	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr6:45389301-45392277	MCF-7	breast:	n/a	n/a
20	POLR2A	chr6:45390675-45391576	U87	brain:	n/a	n/a
21	RAD21	chr6:45390193-45392102	H1-hESC	embryonic stem cell:	n/a	chr6:45391794-45391808 chr6:45392039-45392052 chr6:45390904-45390916 chr6:45390740-45390753 chr6:45391581-45391591
22	CTBP2	chr6:45390579-45392136	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr6:45390836-45391331	MCF-7	breast:	n/a	n/a
24	EGR1	chr6:45390866-45391713	MCF-7	breast:	n/a	chr6:45391435-45391449 chr6:45391435-45391448 chr6:45391524-45391538 chr6:45391523-45391536 chr6:45391435-45391448 chr6:45391525-45391535 chr6:45391434-45391449 chr6:45391523-45391536 chr6:45391438-45391447 chr6:45391523-45391536 chr6:45391524-45391535 chr6:45391525-45391535 chr6:45391431-45391453 chr6:45391526-45391535 chr6:45391523-45391537 chr6:45391435-45391448
25	POLR2A	chr6:45390759-45391352	U87	brain:	n/a	n/a
26	RAD21	chr6:45390874-45391278	H1-hESC	embryonic stem cell:	n/a	chr6:45390904-45390916
27	MXI1	chr6:45389223-45392118	IMR90	lung:	n/a	n/a
28	MYC	chr6:45390599-45391369	NB4	blood:	n/a	n/a
29	POLR2A	chr6:45389241-45392606	NB4	blood:	n/a	n/a
30	BACH1	chr6:45390680-45391324	H1-hESC	embryonic stem cell:	n/a	n/a
31	TEAD4	chr6:45390871-45391124	H1-hESC	embryonic stem cell:	n/a	n/a
32	CHD2	chr6:45390668-45391092	H1-hESC	embryonic stem cell:	n/a	chr6:45391066-45391076
33	MYC	chr6:45390902-45391186	MCF-7	breast:	n/a	n/a
34	POLR2A	chr6:45390154-45391276	Gliobla	brain:	n/a	n/a
35	MAX	chr6:45390733-45391244	H1-hESC	embryonic stem cell:	n/a	n/a
36	SIN3A	chr6:45390610-45391832	H1-hESC	embryonic stem cell:	n/a	chr6:45391573-45391586 chr6:45391337-45391350
37	POLR2A	chr6:45390738-45391066	MCF-7	breast:	n/a	n/a
38	POLR2A	chr6:45390675-45391618	U87	brain:	n/a	n/a
39	POLR2A	chr6:45390287-45391407	MCF-7	breast:	n/a	n/a
40	MAX	chr6:45390283-45391175	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAZ	chr6:45389048-45392554	IMR90	lung:	n/a	chr6:45391434-45391444 chr6:45389137-45389147
42	EGR1	chr6:45390569-45391738	H1-hESC	embryonic stem cell:	n/a	chr6:45391435-45391449 chr6:45391435-45391448 chr6:45391524-45391538 chr6:45391523-45391536 chr6:45391435-45391448 chr6:45391525-45391535 chr6:45391434-45391449 chr6:45391523-45391536 chr6:45391438-45391447 chr6:45391523-45391536 chr6:45391524-45391535 chr6:45391525-45391535 chr6:45391431-45391453 chr6:45391526-45391535 chr6:45391523-45391537 chr6:45391435-45391448

No.	Distal block	Cell Line	Cell type
1	chr6:45390553..45391208-chr6:45683235..45684062,2	MCF-7	breast:
2	chr6:45369759..45372221-chr6:45390852..45393677,2	K562	blood:
3	chr6:44626505..44628712-chr6:45390567..45392142,2	MCF-7	breast:
4	chr6:44700126..44702193-chr6:45390797..45392676,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271857	TF binding region

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

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

rs_ID	r²[population]
rs1004130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498760	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11963804	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11966462	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11968177	0.80[ASN][1000 genomes]
rs17209846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17209853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17209874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17209881	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288355	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17288376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17288390	0.83[ASN][1000 genomes]
rs17288397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805811	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413613	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56789892	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57013196	0.80[ASN][1000 genomes]
rs58571027	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59397804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61467394	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6921145	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7768466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3495915	chr6:45388574-45392472	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3495916	chr6:45388574-45392472	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45387000-45391800	Bivalent Enhancer	Fetal Brain Male	brain
2	chr6:45387000-45392200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:45387400-45391000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
4	chr6:45388200-45391800	Active TSS	Ovary	ovary
5	chr6:45388200-45392000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:45388200-45392000	Active TSS	NHDF-Ad	bronchial
7	chr6:45388200-45392400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:45388400-45393400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:45388600-45391000	Active TSS	Brain Angular Gyrus	brain
10	chr6:45388600-45391600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:45388600-45391800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr6:45388600-45392000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr6:45388600-45392200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:45388600-45392800	Active TSS	HSMM	muscle
15	chr6:45388600-45393000	Active TSS	NHLF	lung
16	chr6:45388800-45391400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:45388800-45391800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:45388800-45391800	Active TSS	Muscle Satellite Cultured Cells	--
19	chr6:45388800-45392000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr6:45388800-45392400	Active TSS	HSMMtube	muscle
21	chr6:45389000-45391200	Active TSS	HMEC	breast
22	chr6:45389000-45391800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:45389000-45392200	Active TSS	Osteobl	bone
24	chr6:45389000-45392400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr6:45389000-45392400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:45389000-45392600	Active TSS	Monocytes-CD14+_RO01746	blood
27	chr6:45389200-45391000	Bivalent/Poised TSS	Fetal Brain Female	brain
28	chr6:45389200-45391600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:45389200-45391600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
30	chr6:45389200-45391600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
31	chr6:45389200-45391800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:45389200-45391800	Active TSS	NH-A	brain
33	chr6:45389200-45392000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr6:45389200-45392000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr6:45389200-45392000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:45389200-45392000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:45389200-45392000	Active TSS	Brain Substantia Nigra	brain
38	chr6:45389200-45392000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
39	chr6:45389200-45392000	Active TSS	NHEK	skin
40	chr6:45389200-45392200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr6:45389200-45392400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
42	chr6:45389200-45392400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr6:45389400-45391000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr6:45389400-45391000	Active TSS	Gastric	stomach
45	chr6:45389400-45391000	Bivalent/Poised TSS	Psoas Muscle	Psoas
46	chr6:45389400-45391000	Active TSS	A549	lung
47	chr6:45389400-45391200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:45389400-45391200	Bivalent/Poised TSS	HepG2	liver
49	chr6:45389400-45391400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:45389400-45391400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links