Variant report

Variant	rs5945429
Chromosome Location	chrX:153693811-153693812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chrX:153625628..153632278-chrX:153692369..153698999,8	K562	blood:
2	chrX:153691004..153695395-chrX:153711545..153717567,7	MCF-7	breast:
3	chrX:153625816..153632596-chrX:153691104..153698525,12	K562	blood:
4	X:153614328-153625659..X:153681712-153701576	Hela-S3	cervix:
5	X:153681712-153701576..X:153719993-153730954	Hela-S3	cervix:
6	chrX:153693608..153695809-chrX:153706711..153708953,2	K562	blood:
7	X:153657611-153671976..X:153681712-153701576	Hela-S3	cervix:
8	chrX:153596642..153600094-chrX:153690004..153694161,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000147403	Chromatin interaction
ENSG00000013563	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000071553	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000102178	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000264783	Chromatin interaction
ENSG00000203879	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000196976	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1050047	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs12392447	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs2070822	0.89[ASW][hapmap]
rs2071429	0.82[CEU][hapmap]
rs2315325	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs2472393	0.89[ASW][hapmap];0.82[CEU][hapmap]
rs4542114	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs4898389	0.80[ASW][hapmap];0.82[CEU][hapmap]
rs5945100	0.82[CEU][hapmap]
rs5945195	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap]
rs5945431	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs5945433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs5945434	1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs5986979	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs5986981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs5987266	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs5987267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs7051615	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs7057286	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs7886727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153686000-153702000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
2	chrX:153687000-153702400	ZNF genes & repeats	Fetal Brain Female	brain
3	chrX:153687400-153706600	Weak transcription	Liver	Liver
4	chrX:153687600-153706600	Weak transcription	Psoas Muscle	Psoas
5	chrX:153687800-153706400	Weak transcription	A549	lung
6	chrX:153688000-153706600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chrX:153688000-153706600	Weak transcription	Fetal Kidney	kidney
8	chrX:153688200-153698200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chrX:153688200-153705200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chrX:153688200-153706400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chrX:153688400-153694200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chrX:153688400-153694200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chrX:153688400-153694800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chrX:153688400-153694800	Weak transcription	Small Intestine	intestine
15	chrX:153688400-153700000	Weak transcription	HepG2	liver
16	chrX:153688400-153701000	Weak transcription	Stomach Mucosa	stomach
17	chrX:153688400-153702200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chrX:153688400-153702400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chrX:153688400-153702800	ZNF genes & repeats	Fetal Stomach	stomach
20	chrX:153688400-153705400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chrX:153688400-153706400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chrX:153688400-153706400	Weak transcription	HMEC	breast
23	chrX:153688400-153706600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chrX:153688400-153706600	Weak transcription	HUVEC	blood vessel
25	chrX:153688600-153694000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chrX:153688600-153694200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chrX:153688600-153694400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
28	chrX:153688600-153702400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chrX:153688600-153705400	Weak transcription	K562	blood
30	chrX:153688600-153705600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chrX:153688800-153694600	Weak transcription	Colonic Mucosa	Colon
32	chrX:153688800-153698400	Weak transcription	NH-A	brain
33	chrX:153688800-153700400	Strong transcription	Fetal Intestine Large	intestine
34	chrX:153688800-153700400	Strong transcription	Fetal Intestine Small	intestine
35	chrX:153688800-153700400	Strong transcription	Thymus	Thymus
36	chrX:153688800-153702000	Strong transcription	Gastric	stomach
37	chrX:153688800-153702000	Strong transcription	Spleen	Spleen
38	chrX:153688800-153702200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chrX:153688800-153702200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chrX:153688800-153702800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chrX:153688800-153706400	Weak transcription	HSMMtube	muscle
42	chrX:153689000-153694400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chrX:153689000-153696200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chrX:153689000-153699600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chrX:153689000-153700200	Strong transcription	Adipose Nuclei	Adipose
46	chrX:153689000-153701000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chrX:153689000-153701000	Strong transcription	Fetal Muscle Leg	muscle
48	chrX:153689000-153702000	Strong transcription	NHLF	lung
49	chrX:153689000-153702800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chrX:153689200-153700400	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links