Variant report

Variant	rs17087358
Chromosome Location	chr4:57850695-57850696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57849127..57850775-chr4:57862388..57864850,2	K562	blood:
2	chr4:57848130..57850979-chr4:57885683..57887962,2	K562	blood:
3	chr4:57849127..57851147-chr4:57863350..57865487,2	K562	blood:
4	chr4:57849114..57851470-chr4:57866273..57869117,2	K562	blood:
5	chr4:57847527..57849310-chr4:57850020..57851620,2	MCF-7	breast:
6	chr4:57842821..57845222-chr4:57848302..57852353,5	MCF-7	breast:
7	chr4:57773779..57775624-chr4:57849367..57852363,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000084092	Chromatin interaction
ENSG00000251703	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000047315	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10016108	1.00[CHB][hapmap]
rs11133472	1.00[CHB][hapmap]
rs11573041	1.00[CHB][hapmap]
rs11573128	1.00[CHB][hapmap];0.84[MEX][hapmap]
rs11732394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113032	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13123018	0.85[ASN][1000 genomes]
rs13125082	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs13128671	0.85[ASN][1000 genomes]
rs13130604	0.85[ASN][1000 genomes]
rs13146090	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs13152711	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618761	1.00[CHB][hapmap]
rs17183291	1.00[CHB][hapmap]
rs1718846	1.00[CHB][hapmap]
rs1718848	1.00[CHB][hapmap]
rs34855462	0.86[EUR][1000 genomes]
rs34948796	0.86[EUR][1000 genomes]
rs35185186	0.85[ASN][1000 genomes]
rs4109037	1.00[CHB][hapmap]
rs41495551	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap]
rs4865166	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865176	1.00[CHB][hapmap]
rs4865177	1.00[CHB][hapmap]
rs62310292	1.00[ASN][1000 genomes]
rs62310298	0.86[EUR][1000 genomes]
rs66619445	0.85[ASN][1000 genomes]
rs67541678	0.86[EUR][1000 genomes]
rs7656865	1.00[CHB][hapmap]
rs7661194	0.80[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap]
rs7685791	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9055	0.91[CEU][hapmap];0.85[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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17087358	RP11-738E22.3	cis	Esophagus Mucosa	GTEx
rs17087358	TXNDC9	cis	parietal	SCAN
rs17087358	IGFBP7	cis	multi-tissue	Pritchard
rs17087358	POLR2B	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57846000-57852000	Weak transcription	Aorta	Aorta
2	chr4:57846000-57853600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:57846000-57855600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:57846000-57881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:57846200-57850800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:57846200-57851400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr4:57846200-57851800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:57846200-57851800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:57846200-57851800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:57846200-57853000	Weak transcription	Fetal Kidney	kidney
11	chr4:57846200-57853600	Weak transcription	Esophagus	oesophagus
12	chr4:57846200-57861600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:57846200-57861800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:57846600-57851800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:57846600-57852200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:57846600-57853200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:57846600-57861200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:57846800-57851200	Weak transcription	Lung	lung
19	chr4:57846800-57852000	Weak transcription	NHDF-Ad	bronchial
20	chr4:57846800-57852200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:57846800-57852600	Weak transcription	HSMMtube	muscle
22	chr4:57846800-57900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:57847000-57851400	Weak transcription	Right Atrium	heart
24	chr4:57847000-57851600	Weak transcription	Placenta	Placenta
25	chr4:57847000-57851600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:57847000-57853000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:57847000-57853800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:57847000-57853800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:57847000-57861600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:57847200-57851200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr4:57847200-57851400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:57847200-57851400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:57847200-57851800	Weak transcription	Brain Anterior Caudate	brain
34	chr4:57847200-57851800	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:57847200-57851800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr4:57847200-57853000	Weak transcription	Colonic Mucosa	Colon
37	chr4:57847200-57853400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:57847200-57853600	Weak transcription	Spleen	Spleen
39	chr4:57847400-57851200	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:57847600-57851600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr4:57847600-57851800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr4:57847600-57853800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:57847600-57856000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr4:57847800-57853600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:57848000-57851600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:57848000-57852000	Weak transcription	Brain Substantia Nigra	brain
47	chr4:57848000-57861400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr4:57848200-57851800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr4:57848200-57852000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:57848200-57852600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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