Variant report

Variant	rs6492946
Chromosome Location	chr15:40732111-40732112
allele	A/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	POLR2A	chr15:40731604-40732171	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr15:40731395-40734925	SK-N-SH	brain:	n/a	n/a
3	RCOR1	chr15:40731733-40732168	K562	blood:	n/a	n/a
4	POLR2A	chr15:40728064-40734370	K562	blood:	n/a	n/a
5	SIN3A	chr15:40731624-40734535	H1-hESC	embryonic stem cell:	n/a	chr15:40732000-40732008 chr15:40733072-40733085 chr15:40734006-40734017 chr15:40732439-40732450
6	POLR2A	chr15:40731613-40732513	K562	blood:	n/a	n/a
7	TAL1	chr15:40732100-40732408	K562	blood:	n/a	n/a
8	POLR2A	chr15:40732084-40732473	MCF-7	breast:	n/a	n/a
9	POLR2A	chr15:40731974-40733265	PFSK-1	brain:	n/a	n/a
10	CUX1	chr15:40731842-40732136	K562	blood:	n/a	n/a
11	MAX	chr15:40731731-40732111	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr15:40731312-40733266	H1-hESC	embryonic stem cell:	n/a	n/a
13	BACH1	chr15:40731650-40732156	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF1	chr15:40731690-40732128	H1-hESC	embryonic stem cell:	n/a	n/a
15	TCF7L2	chr15:40731986-40732552	HCT-116	colon:	n/a	n/a
16	TCF12	chr15:40731717-40733275	ECC-1	luminal epithelium:	n/a	chr15:40732643-40732653 chr15:40732011-40732018
17	POLR2A	chr15:40731422-40733782	K562	blood:	n/a	n/a
18	POLR2A	chr15:40732108-40732452	MCF-7	breast:	n/a	n/a
19	HEY1	chr15:40731639-40732702	K562	blood:	n/a	n/a
20	POLR2A	chr15:40732021-40732592	U87	brain:	n/a	n/a
21	MYC	chr15:40731745-40733764	K562	blood:	n/a	chr15:40732747-40732757 chr15:40732940-40732950
22	SIN3AK20	chr15:40731647-40732901	H1-hESC	embryonic stem cell:	n/a	n/a
23	RCOR1	chr15:40731458-40733568	K562	blood:	n/a	n/a
24	RFX5	chr15:40731436-40734230	SK-N-SH	brain:	n/a	chr15:40733095-40733104 chr15:40732991-40733000 chr15:40732189-40732203
25	UBTF	chr15:40731560-40732755	K562	blood:	n/a	n/a
26	TCF7L2	chr15:40731839-40732518	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr15:40730936-40733250	SK-N-MC	brain:	n/a	n/a
28	CCNT2	chr15:40731590-40732277	K562	blood:	n/a	chr15:40731867-40731876
29	POLR2A	chr15:40730497-40732956	K562	blood:	n/a	n/a
30	POLR2A	chr15:40731737-40732531	K562	blood:	n/a	n/a
31	TEAD4	chr15:40731656-40732434	K562	blood:	n/a	n/a
32	CHD2	chr15:40731800-40732129	K562	blood:	n/a	n/a
33	MAZ	chr15:40732103-40732431	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:40732058-40732497	K562	blood:	n/a	n/a
35	POLR2A	chr15:40731546-40733944	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr15:40731682-40732150	H1-hESC	embryonic stem cell:	n/a	n/a
37	ELF1	chr15:40731430-40732345	GM12878	blood:	n/a	n/a
38	SMC3	chr15:40731700-40732332	Hela-S3	cervix:	n/a	chr15:40731981-40731989
39	ZKSCAN1	chr15:40731679-40732636	Hela-S3	cervix:	n/a	n/a
40	TBP	chr15:40731718-40732536	K562	blood:	n/a	n/a
41	POLR2A	chr15:40731670-40733548	K562	blood:	n/a	n/a
42	POLR2A	chr15:40731597-40733761	K562	blood:	n/a	n/a
43	ZNF263	chr15:40732037-40732518	HEK293-T-REx	kidney:	n/a	n/a
44	RAD21	chr15:40731620-40732173	H1-hESC	embryonic stem cell:	n/a	chr15:40731981-40731990 chr15:40731806-40731819
45	BHLHE40	chr15:40732079-40732480	K562	blood:	n/a	n/a
46	ZBTB7A	chr15:40732059-40734732	K562	blood:	n/a	chr15:40732240-40732247 chr15:40733668-40733677 chr15:40733498-40733505
47	ZBTB7A	chr15:40731691-40733091	ECC-1	luminal epithelium:	n/a	chr15:40732240-40732247
48	MYC	chr15:40731828-40733713	K562	blood:	n/a	chr15:40732747-40732757 chr15:40732940-40732950
49	EGR1	chr15:40732049-40732506	K562	blood:	n/a	chr15:40732296-40732307 chr15:40732395-40732408
50	MAX	chr15:40731731-40733706	K562	blood:	n/a	chr15:40732747-40732757 chr15:40732940-40732950

No.	Distal block	Cell Line	Cell type
1	chr15:40731663..40736686-chr15:40795056..40800792,8	K562	blood:
2	chr15:40731823..40734826-chr15:40760868..40766207,7	K562	blood:
3	chr15:40729975..40738939-chr15:40745780..40750666,13	K562	blood:
4	chr15:40659428..40662346-chr15:40732080..40734388,2	MCF-7	breast:
5	chr15:40731340..40734041-chr15:41045866..41047695,2	K562	blood:
6	chr15:40731621..40739951-chr15:40753297..40765462,23	K562	blood:
7	chr15:40730539..40734458-chr15:40797952..40800684,3	K562	blood:
8	chr15:40731794..40734704-chr15:40761511..40763222,2	MCF-7	breast:

Variant related genes	Relation type
BAHD1	TF binding region
ENSG00000137824	Chromatin interaction
ENSG00000259368	Chromatin interaction
ENSG00000259364	Chromatin interaction
ENSG00000259211	Chromatin interaction
ENSG00000140320	Chromatin interaction
ENSG00000140323	Chromatin interaction
ENSG00000259536	Chromatin interaction
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs14363	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1869906	1.00[EUR][1000 genomes]
rs55984256	1.00[EUR][1000 genomes]
rs56010221	1.00[EUR][1000 genomes]
rs56020318	1.00[EUR][1000 genomes]
rs56908156	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57134155	1.00[EUR][1000 genomes]
rs58042425	1.00[EUR][1000 genomes]
rs58870954	1.00[EUR][1000 genomes]
rs58903833	1.00[EUR][1000 genomes]
rs61579851	1.00[EUR][1000 genomes]
rs61678895	1.00[EUR][1000 genomes]
rs6492943	1.00[EUR][1000 genomes]
rs6492948	1.00[EUR][1000 genomes]
rs6492949	1.00[EUR][1000 genomes]
rs7162308	1.00[EUR][1000 genomes]
rs7164094	1.00[EUR][1000 genomes]
rs7165233	1.00[EUR][1000 genomes]
rs7165670	1.00[EUR][1000 genomes]
rs7168197	1.00[EUR][1000 genomes]
rs7173079	1.00[EUR][1000 genomes]
rs7173239	1.00[EUR][1000 genomes]
rs7175153	1.00[EUR][1000 genomes]
rs7176418	1.00[EUR][1000 genomes]
rs7182052	1.00[EUR][1000 genomes]
rs73383123	1.00[EUR][1000 genomes]
rs73383129	1.00[EUR][1000 genomes]
rs73385108	1.00[EUR][1000 genomes]
rs73385110	1.00[EUR][1000 genomes]
rs73385112	1.00[EUR][1000 genomes]
rs73385114	1.00[EUR][1000 genomes]
rs74011172	1.00[EUR][1000 genomes]
rs74011173	1.00[EUR][1000 genomes]
rs74011174	1.00[EUR][1000 genomes]
rs8023956	1.00[EUR][1000 genomes]
rs8025846	1.00[EUR][1000 genomes]
rs8033915	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8034169	1.00[EUR][1000 genomes]
rs8036383	1.00[ASN][1000 genomes]
rs8037881	1.00[EUR][1000 genomes]
rs8038243	1.00[EUR][1000 genomes]
rs8039298	1.00[EUR][1000 genomes]
rs8040231	1.00[EUR][1000 genomes]
rs9672591	1.00[EUR][1000 genomes]
rs9672893	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3442593	chr15:40731460-40735058	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40729200-40732200	Bivalent Enhancer	Fetal Lung	lung
2	chr15:40730800-40732400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr15:40731000-40732400	Flanking Bivalent TSS/Enh	HepG2	liver
4	chr15:40731200-40732200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:40731200-40732200	Bivalent Enhancer	Fetal Thymus	thymus
6	chr15:40731200-40732800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
7	chr15:40731200-40734800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr15:40731400-40732200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:40731400-40732400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:40731400-40732400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:40731400-40732400	Bivalent Enhancer	Fetal Brain Male	brain
12	chr15:40731400-40732600	Flanking Active TSS	Brain Angular Gyrus	brain
13	chr15:40731400-40732800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:40731400-40736000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:40731600-40732200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr15:40731600-40732200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
17	chr15:40731600-40732200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr15:40731600-40732200	Flanking Active TSS	Pancreas	Pancrea
19	chr15:40731600-40732200	Bivalent Enhancer	Stomach Mucosa	stomach
20	chr15:40731600-40732400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:40731600-40732400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr15:40731600-40732400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:40731600-40732400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:40731600-40732600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:40731600-40732600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:40731600-40732600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:40731600-40732600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
28	chr15:40731600-40732800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:40731600-40732800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:40731600-40732800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
31	chr15:40731600-40734800	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr15:40731600-40735000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr15:40731600-40735200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:40731800-40732200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr15:40731800-40732200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:40731800-40732200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:40731800-40732200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr15:40731800-40732200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:40731800-40732200	Flanking Active TSS	Ovary	ovary
40	chr15:40731800-40732200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
41	chr15:40731800-40732400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:40731800-40732400	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr15:40731800-40732400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:40731800-40732600	Flanking Bivalent TSS/Enh	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:40731800-40732600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:40731800-40732600	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr15:40731800-40732600	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr15:40731800-40732600	Flanking Active TSS	Esophagus	oesophagus
49	chr15:40731800-40732600	Flanking Bivalent TSS/Enh	Placenta	Placenta
50	chr15:40731800-40732600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links