Variant report

Variant	rs4236558
Chromosome Location	chr7:101539732-101539733
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101537245..101539830-chr7:101556041..101558710,2	K562	blood:
2	chr7:101538143..101540149-chr7:101548587..101550920,2	MCF-7	breast:
3	chr7:101534339..101537271-chr7:101538707..101540826,3	K562	blood:

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10270083	0.93[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2906656	0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2906719	1.00[JPT][hapmap]
rs2906721	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs2906743	1.00[JPT][hapmap]
rs2906748	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs2970463	1.00[JPT][hapmap]
rs2970464	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs2970469	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2970470	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs2970495	0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs4354243	1.00[JPT][hapmap]
rs4412307	0.91[CEU][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4727512	0.86[MEX][hapmap];0.84[TSI][hapmap]
rs6465837	0.85[YRI][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	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4236558	NAPEPLD	cis	parietal	SCAN
rs4236558	ARPC1B	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101523200-101543200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:101526000-101540400	Weak transcription	Aorta	Aorta
3	chr7:101526400-101542200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:101526800-101543000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:101527000-101543000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:101527000-101543000	Weak transcription	NHEK	skin
7	chr7:101527200-101542200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:101528600-101555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:101528800-101544000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:101529400-101543000	Weak transcription	Brain Substantia Nigra	brain
11	chr7:101529400-101554200	Weak transcription	Primary T cells from cord blood	blood
12	chr7:101530600-101559800	Weak transcription	GM12878-XiMat	blood
13	chr7:101531000-101545000	Weak transcription	Gastric	stomach
14	chr7:101531000-101548000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr7:101531400-101543000	Weak transcription	Placenta	Placenta
16	chr7:101531400-101554600	Weak transcription	Hela-S3	cervix
17	chr7:101533600-101539800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr7:101533800-101559000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:101534200-101546600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:101535000-101544800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:101535400-101554400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:101535600-101554200	Weak transcription	HepG2	liver
23	chr7:101535600-101554600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:101535800-101541000	Weak transcription	Fetal Kidney	kidney
25	chr7:101535800-101541200	Weak transcription	Adipose Nuclei	Adipose
26	chr7:101535800-101543200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:101535800-101543200	Weak transcription	HSMMtube	muscle
28	chr7:101535800-101555200	Weak transcription	Liver	Liver
29	chr7:101535800-101555600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr7:101536000-101541000	Weak transcription	NHDF-Ad	bronchial
31	chr7:101536000-101541200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:101536000-101541200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:101536000-101542400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr7:101536000-101543000	Weak transcription	HSMM	muscle
35	chr7:101536000-101543600	Weak transcription	A549	lung
36	chr7:101536200-101541200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:101536200-101541200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:101536800-101543800	Weak transcription	Brain Germinal Matrix	brain
39	chr7:101537000-101541000	Weak transcription	Fetal Lung	lung
40	chr7:101537000-101543400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:101537000-101543600	Weak transcription	Ovary	ovary
42	chr7:101537000-101547600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr7:101537000-101547600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr7:101537000-101554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:101537000-101554600	Weak transcription	Fetal Intestine Large	intestine
46	chr7:101537200-101540600	Weak transcription	Fetal Intestine Small	intestine
47	chr7:101537400-101542200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:101537600-101541200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:101537600-101559000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:101538600-101539800	Enhancers	Right Ventricle	heart

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