Variant report

Variant	rs2070643
Chromosome Location	chrX:153677700-153677701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chrX:153677600-153677750	HEK293	kidney:	n/a	n/a
2	RAD21	chrX:153677471-153677704	SK-N-SH_RA	brain:	n/a	n/a
3	RAD21	chrX:153677512-153677723	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	X:153614328-153625659..X:153676883-153681712	GM12878	blood:
2	chrX:153624495..153633022-chrX:153668916..153678988,23	K562	blood:
3	X:153676883-153681712..X:153719993-153730954	Hela-S3	cervix:
4	chrX:153625461..153628798-chrX:153677584..153681082,4	K562	blood:
5	chrX:153597889..153602863-chrX:153674100..153678441,6	MCF-7	breast:
6	chrX:153625011..153628689-chrX:153675821..153678594,3	MCF-7	breast:

No data

Variant related genes	Relation type
FAM50A	TF binding region
ENSG00000147403	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000013563	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000264783	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1130929	0.88[JPT][hapmap]
rs11593	0.87[JPT][hapmap]
rs12559	0.88[JPT][hapmap]
rs12877	0.88[JPT][hapmap]
rs2051508	0.86[JPT][hapmap]
rs2070807	0.87[JPT][hapmap]
rs2070819	0.86[JPT][hapmap]
rs2070821	0.87[JPT][hapmap]
rs2070825	0.87[JPT][hapmap]
rs2070827	0.87[JPT][hapmap]
rs2070829	0.88[JPT][hapmap]
rs2097214	0.88[JPT][hapmap]
rs2156911	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2239469	0.88[JPT][hapmap]
rs2283762	0.87[JPT][hapmap]
rs28602900	0.87[JPT][hapmap]
rs4898484	0.88[JPT][hapmap]
rs4898494	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6727	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs743547	0.88[JPT][hapmap]
rs743548	0.87[JPT][hapmap]
rs743549	0.87[JPT][hapmap]
rs762514	1.00[CHB][hapmap]
rs7886627	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs915941	0.87[JPT][hapmap]
rs915942	0.87[JPT][hapmap]

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	esv33199	chrX:152864376-153820241	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	276 gene(s)	inside rSNPs	diseases
2	nsv528291	chrX:152864376-153827637	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	277 gene(s)	inside rSNPs	diseases
3	nsv915605	chrX:153333946-153783638	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	nsv519042	chrX:153348431-153829693	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv532962	chrX:153564946-153870337	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	199 gene(s)	inside rSNPs	diseases
6	nsv532963	chrX:153576890-153822717	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	195 gene(s)	inside rSNPs	diseases
7	nsv530281	chrX:153622940-153783184	Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
8	nsv532964	chrX:153622940-153854307	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers 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 miRNA target site	158 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153660400-153679800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
2	chrX:153665600-153680000	ZNF genes & repeats	Fetal Brain Female	brain
3	chrX:153667400-153681200	Weak transcription	Fetal Kidney	kidney
4	chrX:153673000-153679800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
5	chrX:153673200-153678800	Weak transcription	Small Intestine	intestine
6	chrX:153673200-153684200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chrX:153673200-153686800	Weak transcription	Fetal Lung	lung
8	chrX:153673400-153677800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chrX:153673400-153678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chrX:153673400-153685800	Weak transcription	Primary hematopoietic stem cells	blood
11	chrX:153673400-153685800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chrX:153673600-153681000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chrX:153673600-153685800	Weak transcription	Psoas Muscle	Psoas
14	chrX:153673800-153679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chrX:153673800-153685600	Weak transcription	Primary B cells from cord blood	blood
16	chrX:153673800-153685600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chrX:153673800-153685800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chrX:153673800-153685800	Weak transcription	HepG2	liver
19	chrX:153673800-153685800	Weak transcription	HSMM	muscle
20	chrX:153673800-153686000	Weak transcription	HSMMtube	muscle
21	chrX:153673800-153686800	Weak transcription	Stomach Mucosa	stomach
22	chrX:153674000-153677800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chrX:153674000-153679600	Strong transcription	H1 Cell Line	embryonic stem cell
24	chrX:153674000-153681400	Strong transcription	Fetal Intestine Small	intestine
25	chrX:153674000-153681800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chrX:153674000-153685600	Weak transcription	GM12878-XiMat	blood
27	chrX:153674000-153686000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chrX:153674000-153686800	Weak transcription	NHDF-Ad	bronchial
29	chrX:153674200-153677800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chrX:153674200-153679200	Strong transcription	Osteobl	bone
31	chrX:153674200-153679400	Strong transcription	Fetal Intestine Large	intestine
32	chrX:153674200-153680400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chrX:153674200-153685800	Weak transcription	Primary T cells from cord blood	blood
34	chrX:153674400-153678200	Strong transcription	Brain Hippocampus Middle	brain
35	chrX:153674400-153679000	Weak transcription	HUVEC	blood vessel
36	chrX:153674400-153679400	Strong transcription	Fetal Muscle Trunk	muscle
37	chrX:153674400-153679600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chrX:153674400-153679800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chrX:153674400-153685800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chrX:153674400-153685800	Weak transcription	NH-A	brain
41	chrX:153674600-153679800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chrX:153674600-153679800	Strong transcription	Duodenum Mucosa	Duodenum
43	chrX:153674600-153680000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chrX:153674600-153681400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chrX:153674800-153679400	Strong transcription	Ovary	ovary
46	chrX:153674800-153679600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chrX:153674800-153679600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chrX:153674800-153679800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chrX:153674800-153681400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chrX:153674800-153681400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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