Variant report

Variant	rs10250463
Chromosome Location	chr7:127693537-127693538
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10226394	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1035295	0.87[ASN][1000 genomes]
rs322818	0.82[GIH][hapmap]
rs3757758	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757764	0.93[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[ASN][1000 genomes]
rs3808089	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs4473953	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs6960004	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs6968751	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7783102	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs7786786	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs9640847	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10250463	CPA1	cis	parietal	SCAN
rs10250463	C7orf54	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127669400-127726600	Weak transcription	Hela-S3	cervix
2	chr7:127669600-127718200	Weak transcription	A549	lung
3	chr7:127670400-127698800	Weak transcription	Dnd41	blood
4	chr7:127672600-127695400	Weak transcription	Aorta	Aorta
5	chr7:127673000-127697800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:127673200-127712000	Weak transcription	Esophagus	oesophagus
7	chr7:127673800-127703400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:127673800-127715400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:127675200-127695200	Weak transcription	Psoas Muscle	Psoas
10	chr7:127678000-127701200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:127680000-127697600	Weak transcription	Thymus	Thymus
12	chr7:127680400-127698600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:127681000-127716200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:127681200-127718200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:127681600-127714600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr7:127682000-127695400	Weak transcription	NHLF	lung
17	chr7:127682600-127693800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:127682800-127693800	Weak transcription	Fetal Stomach	stomach
19	chr7:127683000-127696200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:127683000-127708800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:127683200-127693800	Weak transcription	Placenta	Placenta
22	chr7:127683200-127695200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:127683200-127696000	Weak transcription	Primary B cells from cord blood	blood
24	chr7:127683200-127700600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:127684400-127694200	Weak transcription	Fetal Intestine Large	intestine
26	chr7:127684400-127701400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:127684600-127694000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:127684600-127697000	Weak transcription	Fetal Thymus	thymus
29	chr7:127685000-127710400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr7:127686000-127696400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:127686400-127695400	Weak transcription	NH-A	brain
32	chr7:127686400-127695800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:127686400-127695800	Weak transcription	Osteobl	bone
34	chr7:127686400-127696000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:127686600-127693800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:127689000-127696400	Weak transcription	Liver	Liver
37	chr7:127689400-127717000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr7:127690000-127696200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:127690000-127697600	Weak transcription	GM12878-XiMat	blood
40	chr7:127690800-127696000	Weak transcription	HepG2	liver
41	chr7:127691400-127699200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:127691600-127693800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr7:127691600-127694600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr7:127691800-127693800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:127691800-127694000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr7:127692000-127693600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr7:127692000-127693800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:127692200-127693600	Enhancers	Primary T cells fromperipheralblood	blood
49	chr7:127692200-127693600	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr7:127692200-127693800	Enhancers	Primary T cells from cord blood	blood

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