Variant report

Variant	rs56179906
Chromosome Location	chr2:47232373-47232374
allele	A/G/T
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	chr2:47232335-47232472	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:47231881-47232653	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47230553..47232834-chr2:47238826..47240399,2	MCF-7	breast:
2	chr2:47211854..47216258-chr2:47229137..47232912,5	K562	blood:
3	chr2:47229922..47232405-chr2:47395571..47398538,2	K562	blood:

Variant related genes	Relation type
TTC7A	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17036039	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58674434	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61155978	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72806575	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72806576	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72806578	0.96[EUR][1000 genomes]
rs72806585	0.93[EUR][1000 genomes]
rs72806588	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv517929	chr2:47217094-47243312	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv518312	chr2:47224927-47262137	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv519217	chr2:47229953-47232495	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47213600-47256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:47214000-47262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:47214200-47235400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:47214600-47242000	Strong transcription	Thymus	Thymus
5	chr2:47214800-47233400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:47214800-47237200	Strong transcription	Primary T cells from cord blood	blood
7	chr2:47214800-47239200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:47215200-47243800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:47215400-47235800	Strong transcription	Primary B cells from cord blood	blood
10	chr2:47215600-47245200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr2:47216400-47241600	Strong transcription	Fetal Thymus	thymus
12	chr2:47219600-47235400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:47222000-47260600	Weak transcription	Small Intestine	intestine
14	chr2:47223200-47235800	Weak transcription	Fetal Kidney	kidney
15	chr2:47223400-47238400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:47223400-47239400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:47223600-47235600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:47223600-47239400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:47223600-47246800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:47223800-47234200	Weak transcription	Psoas Muscle	Psoas
21	chr2:47224200-47233200	Weak transcription	GM12878-XiMat	blood
22	chr2:47224800-47238400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:47226600-47233000	Weak transcription	Liver	Liver
24	chr2:47226800-47232600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:47227000-47232800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:47227200-47233000	Enhancers	Brain Substantia Nigra	brain
27	chr2:47227400-47232400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:47227400-47232800	Enhancers	Brain Anterior Caudate	brain
29	chr2:47227400-47233000	Enhancers	Brain Hippocampus Middle	brain
30	chr2:47227400-47233200	Enhancers	Brain Angular Gyrus	brain
31	chr2:47227400-47234000	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:47228000-47233000	Enhancers	Adipose Nuclei	Adipose
33	chr2:47228400-47233200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:47229000-47233200	Enhancers	Fetal Muscle Leg	muscle
35	chr2:47229200-47232400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:47229200-47233000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:47229200-47233000	Enhancers	Rectal Smooth Muscle	rectum
38	chr2:47229200-47243000	Enhancers	Fetal Brain Male	brain
39	chr2:47229200-47248600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:47229400-47232400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:47229400-47232800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:47229400-47235600	Enhancers	Fetal Brain Female	brain
43	chr2:47229600-47232400	Enhancers	Right Ventricle	heart
44	chr2:47229600-47232800	Genic enhancers	Spleen	Spleen
45	chr2:47229600-47233200	Enhancers	Right Atrium	heart
46	chr2:47229600-47237000	Genic enhancers	Fetal Stomach	stomach
47	chr2:47230000-47232600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:47230200-47234800	Strong transcription	Pancreas	Pancrea
49	chr2:47230200-47235800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:47230200-47236600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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