Variant report

Variant	rs42102
Chromosome Location	chr7:27717716-27717717
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:27716154..27718017-chr7:27726881..27729389,2	K562	blood:
2	chr7:27702507..27704104-chr7:27716962..27719221,3	K562	blood:
3	chr7:27711761..27713688-chr7:27715635..27717751,2	K562	blood:
4	chr7:27702060..27704104-chr7:27716962..27718594,2	K562	blood:
5	chr7:27716474..27720411-chr7:27722310..27724514,4	K562	blood:
6	chr7:27716638..27718426-chr7:27834376..27836195,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106049	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10229483	0.92[CEU][hapmap]
rs42100	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs42101	0.89[ASW][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs42103	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs42105	0.81[AMR][1000 genomes]
rs42107	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs42108	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs42109	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs42110	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs42102	HIBADH	cis	lymphoblastoid	seeQTL
rs42102	HIBADH	cis	parietal	SCAN
rs42102	SLC25A4	trans	parietal	SCAN
rs42102	HIBADH	cis	multi-tissue	Pritchard
rs42102	HIBADH	cis	cerebellum	SCAN
rs42102	TAX1BP1	cis	cerebellum	SCAN
rs42102	AQP1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27715800-27719000	Enhancers	Fetal Intestine Large	intestine
2	chr7:27716000-27719200	Enhancers	Fetal Intestine Small	intestine
3	chr7:27716200-27719600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:27716400-27720800	Enhancers	HepG2	liver
5	chr7:27716800-27719000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:27716800-27719200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:27716800-27719200	Enhancers	Placenta	Placenta
8	chr7:27716800-27719200	Enhancers	HSMM	muscle
9	chr7:27716800-27719800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:27716800-27720000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:27716800-27720000	Enhancers	HMEC	breast
12	chr7:27716800-27720800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:27717000-27718000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:27717000-27718000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:27717000-27718200	Flanking Active TSS	A549	lung
16	chr7:27717000-27718400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr7:27717000-27719000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr7:27717000-27719200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:27717000-27719200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr7:27717000-27719200	Enhancers	Stomach Mucosa	stomach
21	chr7:27717000-27719200	Enhancers	HSMMtube	muscle
22	chr7:27717000-27719200	Enhancers	Osteobl	bone
23	chr7:27717000-27719600	Enhancers	HUVEC	blood vessel
24	chr7:27717200-27718200	Enhancers	Colon Smooth Muscle	Colon
25	chr7:27717200-27718200	Flanking Active TSS	NH-A	brain
26	chr7:27717200-27719200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:27717200-27719600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:27717200-27719600	Enhancers	NHLF	lung
29	chr7:27717400-27718200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr7:27717400-27718600	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr7:27717400-27720400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:27717600-27717800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:27717600-27717800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr7:27717600-27718000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr7:27717600-27718000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr7:27717600-27718000	Flanking Active TSS	Hela-S3	cervix
37	chr7:27717600-27718000	Flanking Active TSS	K562	blood
38	chr7:27717600-27718000	Enhancers	NHEK	skin
39	chr7:27717600-27718200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:27717600-27718200	Enhancers	Rectal Smooth Muscle	rectum
41	chr7:27717600-27721000	Enhancers	NHDF-Ad	bronchial

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