Variant report

Variant	rs58674434
Chromosome Location	chr2:47230755-47230756
allele	C/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	chr2:47229053-47230756	GM12892	blood:	n/a	n/a
2	POLR2A	chr2:47230690-47230941	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:47230117-47230859	GM12892	blood:	n/a	n/a
4	RFX5	chr2:47228920-47231067	SK-N-SH	brain:	n/a	chr2:47229898-47229913 chr2:47229895-47229910 chr2:47229899-47229908 chr2:47229897-47229914 chr2:47229214-47229231 chr2:47229898-47229913 chr2:47229923-47229938 chr2:47229896-47229910 chr2:47229898-47229913 chr2:47229897-47229905 chr2:47229926-47229935
5	POLR2A	chr2:47230141-47231169	GM12892	blood:	n/a	n/a
6	NFATC1	chr2:47230202-47230766	GM12878	blood:	n/a	n/a
7	MXI1	chr2:47228934-47230772	SK-N-SH	brain:	n/a	chr2:47229899-47229914 chr2:47229897-47229912

No.	Distal block	Cell Line	Cell type
1	chr2:47227228..47229377-chr2:47229384..47232229,2	K562	blood:
2	chr2:47230553..47232834-chr2:47238826..47240399,2	MCF-7	breast:
3	chr2:47229613..47231414-chr2:47402235..47404640,2	K562	blood:
4	chr2:47230013..47232096-chr2:47242841..47244981,3	K562	blood:
5	chr2:47229727..47232211-chr2:47401787..47404061,4	MCF-7	breast:
6	chr2:47211854..47216258-chr2:47229137..47232912,5	K562	blood:
7	chr2:47229922..47232405-chr2:47395571..47398538,2	K562	blood:

Variant related genes	Relation type
TTC7A	TF binding region
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13399571	1.00[ASN][1000 genomes]
rs17036022	1.00[ASN][1000 genomes]
rs17036033	1.00[ASN][1000 genomes]
rs17036039	0.93[EUR][1000 genomes]
rs17480869	1.00[ASN][1000 genomes]
rs17480988	1.00[ASN][1000 genomes]
rs17481037	1.00[ASN][1000 genomes]
rs17481209	1.00[ASN][1000 genomes]
rs17540157	1.00[ASN][1000 genomes]
rs17540219	1.00[ASN][1000 genomes]
rs17540462	1.00[ASN][1000 genomes]
rs3814035	0.86[ASN][1000 genomes]
rs55641002	1.00[ASN][1000 genomes]
rs55805005	1.00[ASN][1000 genomes]
rs55824224	0.86[ASN][1000 genomes]
rs56179906	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56186415	0.87[ASN][1000 genomes]
rs58637066	1.00[ASN][1000 genomes]
rs59785154	0.86[ASN][1000 genomes]
rs60732316	0.86[ASN][1000 genomes]
rs61155978	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6726941	0.86[ASN][1000 genomes]
rs6727430	1.00[ASN][1000 genomes]
rs6727529	1.00[ASN][1000 genomes]
rs6751599	1.00[ASN][1000 genomes]
rs6751621	1.00[ASN][1000 genomes]
rs6754795	1.00[ASN][1000 genomes]
rs6755001	1.00[ASN][1000 genomes]
rs72806525	0.86[ASN][1000 genomes]
rs72806536	0.86[ASN][1000 genomes]
rs72806537	0.86[ASN][1000 genomes]
rs72806538	0.86[ASN][1000 genomes]
rs72806541	0.86[ASN][1000 genomes]
rs72806558	1.00[ASN][1000 genomes]
rs72806562	1.00[ASN][1000 genomes]
rs72806571	1.00[ASN][1000 genomes]
rs72806575	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72806576	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72806578	0.93[EUR][1000 genomes]
rs72806585	0.90[EUR][1000 genomes]
rs72806588	0.83[EUR][1000 genomes]
rs7564728	1.00[ASN][1000 genomes]
rs7576915	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv521400	chr2:47229953-47231215	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	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:125 , 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	chr2:47214200-47231000	Weak transcription	K562	blood
4	chr2:47214200-47235400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:47214600-47242000	Strong transcription	Thymus	Thymus
6	chr2:47214800-47231200	Weak transcription	HUVEC	blood vessel
7	chr2:47214800-47233400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:47214800-47237200	Strong transcription	Primary T cells from cord blood	blood
9	chr2:47214800-47239200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:47215200-47243800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:47215400-47235800	Strong transcription	Primary B cells from cord blood	blood
12	chr2:47215600-47245200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr2:47216400-47241600	Strong transcription	Fetal Thymus	thymus
14	chr2:47219600-47235400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:47222000-47260600	Weak transcription	Small Intestine	intestine
16	chr2:47223200-47235800	Weak transcription	Fetal Kidney	kidney
17	chr2:47223400-47238400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:47223400-47239400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:47223600-47235600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:47223600-47239400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:47223600-47246800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:47223800-47234200	Weak transcription	Psoas Muscle	Psoas
23	chr2:47224200-47233200	Weak transcription	GM12878-XiMat	blood
24	chr2:47224800-47238400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:47226600-47233000	Weak transcription	Liver	Liver
26	chr2:47226800-47231000	Weak transcription	Aorta	Aorta
27	chr2:47226800-47232000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:47226800-47232600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:47227000-47232800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:47227200-47233000	Enhancers	Brain Substantia Nigra	brain
31	chr2:47227400-47232000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:47227400-47232200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr2:47227400-47232400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:47227400-47232800	Enhancers	Brain Anterior Caudate	brain
35	chr2:47227400-47233000	Enhancers	Brain Hippocampus Middle	brain
36	chr2:47227400-47233200	Enhancers	Brain Angular Gyrus	brain
37	chr2:47227400-47234000	Enhancers	Brain Cingulate Gyrus	brain
38	chr2:47228000-47233000	Enhancers	Adipose Nuclei	Adipose
39	chr2:47228400-47233200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:47229000-47231200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:47229000-47231400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:47229000-47231400	Genic enhancers	Monocytes-CD14+_RO01746	blood
43	chr2:47229000-47231600	Enhancers	Fetal Heart	heart
44	chr2:47229000-47232200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:47229000-47233200	Enhancers	Fetal Muscle Leg	muscle
46	chr2:47229200-47231400	Enhancers	Stomach Mucosa	stomach
47	chr2:47229200-47231600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr2:47229200-47231600	Enhancers	Brain Germinal Matrix	brain
49	chr2:47229200-47231800	Enhancers	NHDF-Ad	bronchial
50	chr2:47229200-47232200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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