Variant report

Variant	rs9904503
Chromosome Location	chr17:45884372-45884373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45882984..45885950-chr17:45891255..45893938,2	MCF-7	breast:
2	chr17:45771011..45773166-chr17:45884072..45886713,2	MCF-7	breast:
3	chr17:45882830..45886365-chr17:45971325..45973276,3	MCF-7	breast:
4	chr17:45725747..45727611-chr17:45884252..45887189,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263766	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000198933	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10428	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs11079797	0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11079799	0.82[JPT][hapmap]
rs16948424	0.86[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs16948662	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2010952	0.89[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2074185	0.82[JPT][hapmap]
rs2074189	0.87[LWK][hapmap]
rs34156395	0.95[EUR][1000 genomes]
rs4793688	0.82[JPT][hapmap]
rs4794224	0.82[JPT][hapmap]
rs59111282	0.95[EUR][1000 genomes]
rs62076106	0.98[EUR][1000 genomes]
rs6503875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7212099	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs7214694	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8078688	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs916798	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs9895764	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9896712	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9897598	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9903904	0.86[ASN][1000 genomes]
rs9915028	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS 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	67 gene(s)	inside rSNPs	diseases
2	nsv908572	chr17:45858487-45900856	Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9904503	CNTNAP1	cis	cerebellum	SCAN
rs9904503	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs9904503	KRTAP4-1	cis	cerebellum	SCAN
rs9904503	SCRN2	cis	Muscle Skeletal	GTEx
rs9904503	CALCOCO2	cis	cerebellum	SCAN
rs9904503	SCRN2	cis	Whole Blood	GTEx
rs9904503	SCRN2	cis	Esophagus Mucosa	GTEx
rs9904503	SCRN2	cis	Esophagus Muscularis	GTEx
rs9904503	SCRN2	cis	lung	GTEx
rs9904503	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs9904503	SCRN2	cis	Adipose Subcutaneous	GTEx
rs9904503	SCRN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45879800-45885000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:45880200-45884600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr17:45880200-45885000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:45881200-45884400	Weak transcription	Primary T cells from cord blood	blood
5	chr17:45881600-45884800	Weak transcription	Primary B cells from cord blood	blood
6	chr17:45881600-45885200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:45881600-45897800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr17:45881800-45884400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:45881800-45884400	Weak transcription	Colonic Mucosa	Colon
10	chr17:45881800-45884400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr17:45882000-45884400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr17:45882000-45884400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr17:45882000-45884600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr17:45882000-45885200	Weak transcription	Stomach Mucosa	stomach
15	chr17:45882000-45887200	Weak transcription	NH-A	brain
16	chr17:45882000-45891800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr17:45882200-45884400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:45882200-45884800	Weak transcription	HepG2	liver
19	chr17:45882200-45886400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr17:45882200-45892000	Weak transcription	Fetal Kidney	kidney
21	chr17:45882400-45884400	Weak transcription	Brain Substantia Nigra	brain
22	chr17:45882400-45884400	Weak transcription	Ovary	ovary
23	chr17:45882400-45884600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:45882400-45884800	Weak transcription	Colon Smooth Muscle	Colon
25	chr17:45882400-45884800	Weak transcription	Small Intestine	intestine
26	chr17:45882400-45886000	Weak transcription	HUVEC	blood vessel
27	chr17:45882600-45884600	Weak transcription	Liver	Liver
28	chr17:45882600-45884600	Weak transcription	Brain Angular Gyrus	brain
29	chr17:45882600-45886600	Weak transcription	Fetal Lung	lung
30	chr17:45882600-45898600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:45882800-45884400	Weak transcription	Brain Germinal Matrix	brain
32	chr17:45882800-45884400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr17:45882800-45884600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr17:45882800-45884600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr17:45882800-45886400	Strong transcription	Fetal Intestine Small	intestine
36	chr17:45883000-45884800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr17:45883000-45890200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr17:45883200-45884600	Weak transcription	Fetal Brain Female	brain
39	chr17:45883200-45884800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr17:45883200-45884800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr17:45883200-45885000	Weak transcription	Aorta	Aorta
42	chr17:45883200-45885000	Weak transcription	Esophagus	oesophagus
43	chr17:45883200-45885200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr17:45883200-45886000	Weak transcription	A549	lung
45	chr17:45883200-45886000	Weak transcription	GM12878-XiMat	blood
46	chr17:45883200-45888600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr17:45883400-45885000	Enhancers	Psoas Muscle	Psoas
48	chr17:45883400-45885200	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr17:45883400-45885800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr17:45883400-45885800	Strong transcription	Gastric	stomach

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