Variant report

Variant	rs649775
Chromosome Location	chr6:33684313-33684314
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	chr6:33684132-33684579	HCT-116	colon:	n/a	n/a
2	TEAD4	chr6:33684072-33684627	HCT-116	colon:	n/a	n/a
3	NFIC	chr6:33684123-33684783	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr6:33684148-33684591	H1-hESC	embryonic stem cell:	n/a	n/a
5	TEAD4	chr6:33684142-33684712	ECC-1	luminal epithelium:	n/a	n/a
6	STAT3	chr6:33684265-33684954	MCF10A-Er-Src	breast:	n/a	chr6:33684382-33684393 chr6:33684870-33684879
7	TEAD4	chr6:33684097-33684745	ECC-1	luminal epithelium:	n/a	n/a
8	FOS	chr6:33684297-33685045	MCF10A-Er-Src	breast:	n/a	chr6:33684869-33684879 chr6:33684871-33684878 chr6:33684869-33684879 chr6:33684869-33684878
9	STAT3	chr6:33684303-33684503	MCF10A-Er-Src	breast:	n/a	chr6:33684382-33684393
10	MYC	chr6:33684014-33684373	MCF10A-Er-Src	breast:	n/a	n/a
11	TEAD4	chr6:33684143-33684651	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYC	chr6:33684017-33684322	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr6:33684228-33685040	MCF10A-Er-Src	breast:	n/a	chr6:33684382-33684393 chr6:33684870-33684879
14	TCF12	chr6:33684050-33684887	ECC-1	luminal epithelium:	n/a	chr6:33684385-33684393 chr6:33684208-33684215
15	TCF12	chr6:33684105-33684745	ECC-1	luminal epithelium:	n/a	chr6:33684385-33684393 chr6:33684208-33684215
16	FOS	chr6:33684244-33684482	MCF10A-Er-Src	breast:	n/a	n/a
17	TEAD4	chr6:33684064-33684625	HCT-116	colon:	n/a	n/a
18	NFIC	chr6:33684062-33684794	ECC-1	luminal epithelium:	n/a	n/a
19	FOS	chr6:33684274-33685063	MCF10A-Er-Src	breast:	n/a	chr6:33684869-33684879 chr6:33684871-33684878 chr6:33684869-33684879 chr6:33684869-33684878
20	STAT3	chr6:33684297-33684506	MCF10A-Er-Src	breast:	n/a	chr6:33684382-33684393
21	FOS	chr6:33684272-33685043	MCF10A-Er-Src	breast:	n/a	chr6:33684869-33684879 chr6:33684871-33684878 chr6:33684869-33684879 chr6:33684869-33684878

No.	Distal block	Cell Line	Cell type
1	chr6:33684071..33687779-chr6:33863332..33865982,3	MCF-7	breast:
2	chr6:33682630..33685096-chr6:33696918..33698480,2	K562	blood:
3	chr6:33683155..33686367-chr6:33732476..33736646,4	MCF-7	breast:
4	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
5	chr6:33683624..33685957-chr6:34119355..34121276,2	MCF-7	breast:
6	chr6:33683560..33685755-chr6:33736435..33739209,2	MCF-7	breast:
7	chr6:33680227..33683293-chr6:33684221..33688907,5	K562	blood:

Variant related genes	Relation type
UQCC2	TF binding region
ENSG00000161904	Chromatin interaction
ENSG00000249346	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2229638	0.84[YRI][hapmap]
rs4711333	1.00[CHD][hapmap]
rs4713647	1.00[CHD][hapmap]
rs485623	1.00[CHD][hapmap]
rs523076	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs525623	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs557559	1.00[CHD][hapmap]
rs559290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560218	1.00[CHD][hapmap]
rs572708	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs62398913	0.93[EUR][1000 genomes]
rs637135	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653825	0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72880503	0.85[EUR][1000 genomes]
rs7757722	1.00[CHD][hapmap]
rs791900	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs942637	1.00[ASW][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33679800-33685000	Weak transcription	Lung	lung
2	chr6:33679800-33685600	Weak transcription	Placenta	Placenta
3	chr6:33680000-33684400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:33680000-33684400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:33680000-33684600	Weak transcription	Fetal Brain Male	brain
6	chr6:33680000-33684600	Weak transcription	Fetal Kidney	kidney
7	chr6:33680000-33684800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:33680000-33684800	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:33680000-33684800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:33680000-33684800	Weak transcription	NHLF	lung
11	chr6:33680000-33685000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:33680000-33685000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:33680000-33685000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:33680000-33685000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:33680000-33685000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr6:33680000-33685000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:33680000-33685200	Weak transcription	Right Atrium	heart
18	chr6:33680000-33686000	Weak transcription	Right Ventricle	heart
19	chr6:33680000-33689400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:33680000-33690000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:33680000-33690200	Weak transcription	Psoas Muscle	Psoas
22	chr6:33680000-33693000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:33680000-33695200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:33680000-33695800	Weak transcription	Spleen	Spleen
25	chr6:33680000-33696200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:33680000-33698400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
28	chr6:33680200-33685200	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:33681600-33685800	Enhancers	HepG2	liver
30	chr6:33681800-33689200	Enhancers	Pancreas	Pancrea
31	chr6:33682600-33686200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:33683000-33686600	Enhancers	Stomach Mucosa	stomach
33	chr6:33683200-33686000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:33683200-33686200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:33683800-33684600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr6:33683800-33685400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:33684000-33684400	Enhancers	Gastric	stomach
38	chr6:33684000-33684600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr6:33684000-33684600	Enhancers	Esophagus	oesophagus
40	chr6:33684000-33685200	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr6:33684000-33685400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:33684000-33686200	Enhancers	Liver	Liver
43	chr6:33684000-33686200	Enhancers	NHEK	skin
44	chr6:33684000-33686600	Enhancers	Left Ventricle	heart
45	chr6:33684000-33687000	Enhancers	HMEC	breast
46	chr6:33684200-33684800	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr6:33684200-33685200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr6:33684200-33685600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr6:33684200-33686000	Weak transcription	Fetal Brain Female	brain
50	chr6:33684200-33687400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links