Variant report

Variant	rs10498725
Chromosome Location	chr6:25455015-25455016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CMAHP-7	chr6:25454750-25455074	NONHSAT108161

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1876372	0.82[JPT][hapmap]
rs1876373	0.82[JPT][hapmap]
rs301398	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs301401	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs395935	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429964	0.85[EUR][1000 genomes]
rs451413	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55946641	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72839015	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912449	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461170	0.84[GIH][hapmap];1.00[JPT][hapmap]
rs9467516	1.00[JPT][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	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
2	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1850810	chr6:25405576-25462543	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10498725	HIST1H2AK	cis	parietal	SCAN
rs10498725	HIST1H2AJ	cis	parietal	SCAN
rs10498725	ABT1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25418800-25462600	Weak transcription	Ovary	ovary
2	chr6:25433400-25472600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:25436200-25481400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:25438200-25472600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:25442000-25455600	Weak transcription	Aorta	Aorta
6	chr6:25443200-25472600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:25446600-25460000	Weak transcription	Fetal Lung	lung
8	chr6:25446800-25493600	Weak transcription	Left Ventricle	heart
9	chr6:25446800-25504400	Weak transcription	Primary B cells from cord blood	blood
10	chr6:25447400-25473200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:25448200-25472600	Weak transcription	Pancreas	Pancrea
12	chr6:25448400-25456600	Weak transcription	Gastric	stomach
13	chr6:25448400-25464400	Weak transcription	Thymus	Thymus
14	chr6:25449000-25462400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:25449000-25463600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:25449400-25515800	Weak transcription	Lung	lung
17	chr6:25449600-25461200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:25449800-25456000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:25450200-25456000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:25450400-25455400	Weak transcription	Fetal Brain Female	brain
21	chr6:25450400-25488400	Weak transcription	Fetal Intestine Large	intestine
22	chr6:25450600-25456000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:25450800-25457800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:25450800-25458400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:25450800-25461600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:25450800-25462600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:25451600-25461000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:25451600-25461400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:25452000-25458800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:25452000-25459600	Weak transcription	Fetal Thymus	thymus
31	chr6:25452200-25456000	Weak transcription	Right Atrium	heart
32	chr6:25452200-25473000	Weak transcription	Fetal Intestine Small	intestine
33	chr6:25452400-25476000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:25452600-25455800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:25452800-25467400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:25453400-25455400	Weak transcription	HSMMtube	muscle
37	chr6:25454200-25455200	Weak transcription	Primary T cells from cord blood	blood
38	chr6:25454200-25455400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:25454200-25472800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:25454400-25455200	Enhancers	HMEC	breast
41	chr6:25454600-25458600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:25454600-25462400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:25454800-25456000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:25454800-25456400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:25454800-25457800	Weak transcription	NHEK	skin
46	chr6:25454800-25458400	Weak transcription	Osteobl	bone
47	chr6:25454800-25458800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr6:25454800-25463600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr6:25455000-25456000	Weak transcription	NHDF-Ad	bronchial
50	chr6:25455000-25457200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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