Variant report

Variant	rs7752524
Chromosome Location	chr6:25310585-25310586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10456320	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs11752017	1.00[JPT][hapmap]
rs11759560	1.00[JPT][hapmap]
rs11759648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12203031	1.00[JPT][hapmap]
rs12203442	1.00[JPT][hapmap]
rs12205303	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211739	1.00[JPT][hapmap]
rs2018839	1.00[LWK][hapmap]
rs2690110	0.94[LWK][hapmap]
rs2744294	0.94[LWK][hapmap]
rs4712910	0.85[YRI][hapmap]
rs6902634	1.00[YRI][hapmap]
rs716796	1.00[JPT][hapmap]
rs760865	1.00[JPT][hapmap]
rs7743997	1.00[YRI][hapmap]
rs7762537	1.00[JPT][hapmap]
rs7764258	1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7767189	1.00[YRI][hapmap]
rs9461151	1.00[JPT][hapmap]
rs9467496	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7752524	PRRX1	trans	lymphoblastoid	seeQTL
rs7752524	HIST1H3C	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:25294200-25311200	Weak transcription	Lung	lung
3	chr6:25298000-25311800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:25301400-25313400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:25301600-25311600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:25302000-25312800	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:25302600-25311200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:25302600-25312400	Weak transcription	Thymus	Thymus
9	chr6:25302800-25312200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:25303200-25311200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:25303200-25311600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:25303200-25314800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:25303400-25311600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:25303400-25315400	Weak transcription	Fetal Kidney	kidney
15	chr6:25303800-25311800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:25303800-25312400	Weak transcription	Adipose Nuclei	Adipose
17	chr6:25304000-25311400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:25304000-25311600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:25304200-25311400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:25305000-25311200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
22	chr6:25305400-25311600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:25305600-25311600	Weak transcription	Fetal Lung	lung
24	chr6:25305600-25311800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:25306600-25311600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
27	chr6:25306800-25311200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:25306800-25311800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:25308400-25311600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:25308600-25312600	Weak transcription	Fetal Heart	heart
31	chr6:25309200-25313400	Weak transcription	Ovary	ovary
32	chr6:25310000-25312400	Enhancers	Small Intestine	intestine
33	chr6:25310000-25312600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:25310200-25310600	Enhancers	HSMMtube	muscle
35	chr6:25310200-25310600	Enhancers	NHLF	lung
36	chr6:25310200-25310800	Enhancers	Brain Anterior Caudate	brain
37	chr6:25310200-25311200	Enhancers	Hela-S3	cervix
38	chr6:25310200-25311800	Enhancers	A549	lung
39	chr6:25310200-25312200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:25310200-25313000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:25310200-25313600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:25310200-25313800	Enhancers	Fetal Intestine Large	intestine
43	chr6:25310200-25314200	Enhancers	Fetal Intestine Small	intestine
44	chr6:25310200-25316800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:25310400-25310600	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr6:25310400-25310600	Enhancers	Aorta	Aorta
47	chr6:25310400-25310600	Enhancers	Right Atrium	heart
48	chr6:25310400-25310600	Enhancers	NH-A	brain
49	chr6:25310400-25310800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:25310400-25311000	Enhancers	Stomach Mucosa	stomach

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