Variant report

Variant	rs6616729
Chromosome Location	chrX:80514952-80514953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:80514794..80516843-chrX:80519998..80521762,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12389790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1372756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1372757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1538351	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1954611	0.84[JPT][hapmap]
rs2027279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2039717	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5959087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5959088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5959857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5959860	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs6524053	1.00[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754822	chrX:80365094-80852865	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:80494200-80523000	Weak transcription	Gastric	stomach
2	chrX:80496200-80518400	Weak transcription	Pancreas	Pancrea
3	chrX:80497400-80534400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chrX:80497800-80525800	Weak transcription	Primary B cells from peripheral blood	blood
5	chrX:80501800-80526000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chrX:80510200-80547400	Weak transcription	Primary B cells from cord blood	blood
7	chrX:80511600-80547000	Weak transcription	Brain Angular Gyrus	brain
8	chrX:80512200-80536800	Weak transcription	Brain Hippocampus Middle	brain
9	chrX:80512400-80517800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chrX:80512600-80539000	Weak transcription	Primary T cells from cord blood	blood
11	chrX:80512800-80516400	Enhancers	Colon Smooth Muscle	Colon
12	chrX:80513200-80515800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chrX:80513400-80515200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chrX:80513600-80515400	Enhancers	Rectal Smooth Muscle	rectum
15	chrX:80513800-80516200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chrX:80514000-80515000	Enhancers	Fetal Stomach	stomach
17	chrX:80514000-80515200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chrX:80514000-80515800	Enhancers	Monocytes-CD14+_RO01746	blood
19	chrX:80514000-80515800	Enhancers	NHLF	lung
20	chrX:80514000-80516400	Enhancers	Stomach Smooth Muscle	stomach
21	chrX:80514000-80517400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chrX:80514000-80518000	Enhancers	NH-A	brain
23	chrX:80514000-80519000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chrX:80514000-80519400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chrX:80514200-80515000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chrX:80514200-80515000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chrX:80514200-80515000	Enhancers	Placenta Amnion	Placenta Amnion
28	chrX:80514200-80515200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chrX:80514200-80515200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chrX:80514200-80515200	Enhancers	HMEC	breast
31	chrX:80514200-80515400	Enhancers	Fetal Heart	heart
32	chrX:80514200-80515600	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chrX:80514200-80515800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chrX:80514200-80515800	Enhancers	Stomach Mucosa	stomach
35	chrX:80514200-80515800	Enhancers	HSMM	muscle
36	chrX:80514200-80515800	Enhancers	NHDF-Ad	bronchial
37	chrX:80514200-80516000	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chrX:80514200-80516200	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chrX:80514200-80517600	Weak transcription	Fetal Lung	lung
40	chrX:80514400-80515400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chrX:80514400-80515800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chrX:80514400-80525800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chrX:80514600-80515000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chrX:80514600-80515200	Enhancers	H1 Cell Line	embryonic stem cell
45	chrX:80514600-80515400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chrX:80514600-80515400	Enhancers	Small Intestine	intestine
47	chrX:80514600-80515400	Enhancers	NHEK	skin
48	chrX:80514600-80515800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chrX:80514600-80515800	Enhancers	Hela-S3	cervix
50	chrX:80514600-80532600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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