Variant report

Variant	rs546088227
Chromosome Location	chr6:71997890-71997891
allele	A/C
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	POU2F2	chr6:71997694-71998083	GM12878	blood:	n/a	n/a
2	USF2	chr6:71997798-71998136	Hela-S3	cervix:	n/a	n/a
3	EBF1	chr6:71997740-71998145	GM12878	blood:	n/a	n/a
4	MTA3	chr6:71997607-71998195	GM12878	blood:	n/a	n/a
5	E2F6	chr6:71997848-71998476	A549	lung:	n/a	chr6:71998384-71998394 chr6:71998318-71998327
6	RFX5	chr6:71997869-71998509	Hela-S3	cervix:	n/a	n/a
7	MAX	chr6:71997865-71998751	MCF-7	breast:	n/a	n/a
8	YY1	chr6:71997764-71998290	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:71997669-71998764	HUVEC	blood vessel:	n/a	n/a
10	MAZ	chr6:71997858-71999980	IMR90	lung:	n/a	n/a
11	PBX3	chr6:71997826-71998011	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:71997764-71999171	GM12878	blood:	n/a	n/a
13	CHD2	chr6:71997795-71998257	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:71997747-71999605	GM19099	blood:	n/a	n/a
15	MAX	chr6:71997808-71998758	NB4	blood:	n/a	n/a
16	MAFK	chr6:71997874-71998166	Hela-S3	cervix:	n/a	n/a
17	TAF1	chr6:71997733-71997929	SK-N-SH	brain:	n/a	n/a
18	CHD2	chr6:71997852-71998706	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr6:71997641-71998711	HUVEC	blood vessel:	n/a	n/a
20	TBP	chr6:71997831-71998137	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr6:71997883-71998750	HCT-116	colon:	n/a	n/a
22	IKZF1	chr6:71997771-71998076	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:71997837-71999136	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr6:71997803-71999251	GM18526	blood:	n/a	n/a
25	ZNF263	chr6:71997455-71999152	HEK293-T-REx	kidney:	n/a	chr6:71998405-71998414 chr6:71997726-71997735
26	MAX	chr6:71997819-71998839	ECC-1	luminal epithelium:	n/a	n/a
27	MXI1	chr6:71997749-71998704	GM12878	blood:	n/a	n/a
28	MAZ	chr6:71997822-71998676	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr6:71997868-71998145	SK-N-SH	brain:	n/a	n/a
30	GTF2F1	chr6:71997860-71998184	Hela-S3	cervix:	n/a	n/a
31	MAZ	chr6:71997768-71998658	GM12878	blood:	n/a	n/a
32	SP1	chr6:71997671-71998138	GM12878	blood:	n/a	chr6:71998082-71998094 chr6:71998079-71998093 chr6:71998082-71998094 chr6:71998083-71998092 chr6:71998089-71998099
33	REST	chr6:71997824-71998826	H1-neurons	neurons:	n/a	chr6:71998068-71998086 chr6:71998391-71998401 chr6:71998071-71998084 chr6:71998154-71998172 chr6:71998067-71998087
34	TCF7L2	chr6:71997884-71998395	Hela-S3	cervix:	n/a	n/a
35	RAD21	chr6:71997789-71998187	Hela-S3	cervix:	n/a	chr6:71998157-71998171
36	POLR2A	chr6:71997843-71998931	Gliobla	brain:	n/a	n/a
37	MYC	chr6:71997815-71998740	NB4	blood:	n/a	n/a
38	POLR2A	chr6:71997845-71999411	GM18951	blood:	n/a	n/a
39	MAX	chr6:71997807-71998780	Hela-S3	cervix:	n/a	n/a
40	SMC3	chr6:71997817-71998679	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr6:71997864-71998721	HCT-116	colon:	n/a	n/a
42	MAX	chr6:71997811-71998808	A549	lung:	n/a	n/a
43	E2F1	chr6:71997807-71999100	Hela-S3	cervix:	n/a	chr6:71998965-71998975 chr6:71998384-71998394 chr6:71998392-71998403 chr6:71998318-71998327
44	POLR2A	chr6:71997860-71999845	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr6:71997809-71999236	MCF10A-Er-Src	breast:	n/a	n/a
46	ZNF143	chr6:71997882-71999069	GM12878	blood:	n/a	chr6:71998324-71998342 chr6:71998399-71998417
47	SPI1	chr6:71997844-71998065	GM12878	blood:	n/a	n/a
48	GATA2	chr6:71997714-71998283	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr6:71997728-71998905	HUVEC	blood vessel:	n/a	n/a
50	RUNX3	chr6:71997676-71998178	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:71997812..71999868-chr6:72020711..72023495,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232295	TF binding region
OGFRL1	TF binding region
ENSG00000232295	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1837685	chr6:71997278-71998880	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	esv1792197	chr6:71997278-71999404	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv1818720	chr6:71997278-71999404	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv1830597	chr6:71997278-71999404	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1795873	chr6:71997278-72005794	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1841286	chr6:71997278-72006512	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3424106	chr6:71997456-72000004	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3385640	chr6:71997681-71999879	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71996800-71998000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr6:71996800-71998200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr6:71997000-71998000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:71997000-71998000	Flanking Active TSS	NHDF-Ad	bronchial
5	chr6:71997000-71998400	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr6:71997000-71998400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:71997000-71999800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:71997000-72002000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:71997200-71998400	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr6:71997200-71998400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:71997200-72000400	Active TSS	A549	lung
12	chr6:71997400-71998000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:71997400-71998000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr6:71997400-71998000	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr6:71997400-71998000	Flanking Active TSS	Brain Angular Gyrus	brain
16	chr6:71997400-71998000	Enhancers	Small Intestine	intestine
17	chr6:71997400-71998200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr6:71997400-71998200	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr6:71997400-71998200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:71997400-71998200	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr6:71997400-71998200	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr6:71997400-71998400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr6:71997400-71999400	Active TSS	Brain Anterior Caudate	brain
24	chr6:71997400-72000000	Active TSS	Rectal Smooth Muscle	rectum
25	chr6:71997400-72000400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:71997600-71998000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr6:71997600-71998000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:71997600-71998000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:71997600-71998000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:71997600-71998000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:71997600-71998000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr6:71997600-71998000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr6:71997600-71998000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:71997600-71998000	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr6:71997600-71998000	Flanking Active TSS	Fetal Kidney	kidney
36	chr6:71997600-71998000	Enhancers	Spleen	Spleen
37	chr6:71997600-71998000	Flanking Active TSS	Hela-S3	cervix
38	chr6:71997600-71998000	Flanking Active TSS	NHLF	lung
39	chr6:71997600-71998000	Flanking Active TSS	Osteobl	bone
40	chr6:71997600-71998200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr6:71997600-71998200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:71997600-71998200	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr6:71997600-71998200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr6:71997600-71998200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr6:71997600-71998200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr6:71997600-71998200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:71997600-71998200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:71997600-71998200	Flanking Active TSS	Liver	Liver
49	chr6:71997600-71998200	Flanking Active TSS	Fetal Brain Male	brain
50	chr6:71997600-71998200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links