Variant report

Variant	rs563751
Chromosome Location	chr6:33552769-33552770
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	MTA3	chr6:33552613-33554260	GM12878	blood:	n/a	n/a
2	CTCF	chr6:33552744-33554121	SK-N-SH	brain:	n/a	chr6:33553589-33553610 chr6:33553587-33553605 chr6:33553664-33553671 chr6:33553580-33553588

No.	Distal block	Cell Line	Cell type
1	chr6:33551460..33554975-chr6:33588078..33592105,4	K562	blood:
2	chr6:33546298..33549471-chr6:33550091..33553469,5	K562	blood:
3	chr6:33550022..33555745-chr6:33586647..33590467,5	MCF-7	breast:
4	chr6:33551901..33555908-chr6:33676752..33679381,5	K562	blood:
5	chr6:33552057..33555351-chr6:33600748..33604007,3	MCF-7	breast:
6	chr6:33384196..33386645-chr6:33552574..33554724,2	MCF-7	breast:
7	chr6:33547287..33549306-chr6:33551969..33553577,2	K562	blood:
8	chr6:33551917..33554088-chr6:33585146..33588477,3	K562	blood:
9	chr6:33384739..33386700-chr6:33551719..33554109,2	MCF-7	breast:

Variant related genes	Relation type
BAK1	TF binding region
ENSG00000096433	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000030110	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs210137	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs210138	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs210144	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs210162	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs375555	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs394199	0.82[CHB][hapmap]
rs407710	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs530878	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900408	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33548200-33553000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr6:33548200-33553000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:33548400-33552800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:33548400-33552800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:33548400-33553000	Weak transcription	Primary B cells from cord blood	blood
6	chr6:33548400-33553000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:33548400-33553000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:33548400-33553000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:33548400-33553000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:33548400-33553000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:33548400-33553000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:33548400-33553000	Weak transcription	Thymus	Thymus
13	chr6:33548400-33553000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:33548400-33553200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr6:33548400-33553200	Weak transcription	Brain Angular Gyrus	brain
16	chr6:33548400-33553200	Weak transcription	HMEC	breast
17	chr6:33548400-33553400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:33548400-33553400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:33548400-33553400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:33548400-33553400	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:33548400-33553400	Weak transcription	Brain Substantia Nigra	brain
22	chr6:33548400-33553400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:33548400-33553400	Weak transcription	Fetal Brain Male	brain
24	chr6:33548400-33553400	Weak transcription	Fetal Heart	heart
25	chr6:33548400-33553400	Weak transcription	Fetal Lung	lung
26	chr6:33548400-33553400	Weak transcription	Placenta	Placenta
27	chr6:33548400-33553400	Weak transcription	HSMMtube	muscle
28	chr6:33548400-33553400	Weak transcription	HUVEC	blood vessel
29	chr6:33548400-33553400	Weak transcription	NH-A	brain
30	chr6:33548400-33553600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:33548400-33553600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:33548400-33553600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:33548400-33553600	Weak transcription	Brain Germinal Matrix	brain
34	chr6:33548400-33553600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:33548400-33553600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr6:33548400-33553600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:33548400-33557000	Weak transcription	HSMM	muscle
38	chr6:33548400-33557200	Weak transcription	NHDF-Ad	bronchial
39	chr6:33548400-33557600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:33548400-33557800	Weak transcription	Right Atrium	heart
41	chr6:33548600-33552800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:33548600-33552800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:33548600-33552800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:33548600-33553000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:33548600-33553000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr6:33548600-33553200	Weak transcription	Adipose Nuclei	Adipose
47	chr6:33548600-33553200	Weak transcription	Fetal Stomach	stomach
48	chr6:33548600-33553400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:33548600-33553400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:33548600-33553400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links