Variant report

Variant	rs12012253
Chromosome Location	chrX:55176004-55176005
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10521478	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs11091385	0.85[CEU][hapmap]
rs12557008	0.84[CEU][hapmap]
rs1494364	1.00[CEU][hapmap]
rs1494365	1.00[CEU][hapmap]
rs1845442	1.00[CEU][hapmap]
rs1874110	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs1874111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4295789	1.00[CEU][hapmap]
rs4826367	0.85[CEU][hapmap]
rs5913792	0.95[CEU][hapmap]
rs5960060	0.84[CEU][hapmap]
rs5960385	0.84[CEU][hapmap]
rs5960401	1.00[CEU][hapmap]
rs5960404	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs5960405	0.88[CEU][hapmap]
rs6611396	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs937280	1.00[CEU][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv6551	chrX:55172471-55185657	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
2	esv2263886	chrX:55172549-55185643	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	esv8458	chrX:55172571-55187606	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
4	esv2409223	chrX:55172597-55185666	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	esv3372451	chrX:55172609-55185644	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
6	esv2295153	chrX:55172641-55187607	Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
7	esv3517503	chrX:55172661-55185600	ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
8	esv3517504	chrX:55172661-55185600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
9	esv3484234	chrX:55172682-55185591	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
10	esv3484235	chrX:55172682-55185591	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
11	esv3362503	chrX:55172686-55185613	ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
12	esv3328985	chrX:55172705-55185583	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
13	esv3326176	chrX:55172706-55185583	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
14	nsv515205	chrX:55172763-55187427	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
15	esv3445398	chrX:55172929-55185618	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
16	esv3345471	chrX:55172949-55185588	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:55167600-55187000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chrX:55169400-55186600	Weak transcription	Fetal Intestine Small	intestine
3	chrX:55169400-55186800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chrX:55170800-55186200	Weak transcription	A549	lung
5	chrX:55171400-55186800	Weak transcription	Stomach Mucosa	stomach
6	chrX:55172600-55186200	Weak transcription	Brain Germinal Matrix	brain
7	chrX:55172800-55176600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chrX:55172800-55176600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chrX:55172800-55176800	Weak transcription	Gastric	stomach
10	chrX:55172800-55176800	Weak transcription	Lung	lung
11	chrX:55172800-55181200	Weak transcription	Esophagus	oesophagus
12	chrX:55172800-55181400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chrX:55172800-55183400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chrX:55172800-55183600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chrX:55172800-55185400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chrX:55172800-55185400	Weak transcription	Brain Substantia Nigra	brain
17	chrX:55172800-55185600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chrX:55172800-55185600	Weak transcription	Primary T cells from cord blood	blood
19	chrX:55172800-55186000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chrX:55172800-55186000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chrX:55172800-55186000	Weak transcription	Liver	Liver
22	chrX:55172800-55186000	Weak transcription	Brain Anterior Caudate	brain
23	chrX:55172800-55186000	Weak transcription	Dnd41	blood
24	chrX:55172800-55186000	Weak transcription	Hela-S3	cervix
25	chrX:55172800-55186200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chrX:55172800-55186200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chrX:55172800-55186600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chrX:55172800-55186600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chrX:55172800-55186600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chrX:55172800-55186600	Weak transcription	Brain Angular Gyrus	brain
31	chrX:55172800-55186600	Weak transcription	Brain Hippocampus Middle	brain
32	chrX:55172800-55186600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chrX:55172800-55186600	Weak transcription	Duodenum Mucosa	Duodenum
34	chrX:55172800-55186600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chrX:55172800-55186600	Weak transcription	Psoas Muscle	Psoas
36	chrX:55172800-55186600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chrX:55172800-55186600	Weak transcription	HMEC	breast
38	chrX:55172800-55186600	Weak transcription	NH-A	brain
39	chrX:55172800-55186600	Weak transcription	NHEK	skin
40	chrX:55172800-55186800	Weak transcription	Brain Cingulate Gyrus	brain
41	chrX:55172800-55186800	Weak transcription	Right Ventricle	heart
42	chrX:55172800-55187000	Weak transcription	Left Ventricle	heart
43	chrX:55172800-55187000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chrX:55175000-55177800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chrX:55175200-55186800	Weak transcription	Stomach Smooth Muscle	stomach
46	chrX:55175400-55176200	Enhancers	Fetal Intestine Large	intestine
47	chrX:55176000-55185400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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