Variant report

Variant	rs17474893
Chromosome Location	chr7:102480757-102480758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102473443..102475589-chr7:102480022..102482918,2	K562	blood:

Variant related genes	Relation type
ENSG00000252643	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10487281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11496066	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12113073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12113759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs17135875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135913	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17135916	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2041094	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215040	0.82[TSI][hapmap]
rs2411061	1.00[CHB][hapmap]
rs3893651	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377880	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4398822	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4610658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55681588	1.00[ASN][1000 genomes]
rs55781834	1.00[ASN][1000 genomes]
rs56146438	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56186316	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56314487	1.00[ASN][1000 genomes]
rs56692051	1.00[ASN][1000 genomes]
rs6955064	1.00[ASN][1000 genomes]
rs6964296	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[LWK][hapmap];0.97[MKK][hapmap];1.00[ASN][1000 genomes]
rs6968036	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs727175	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192015	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192019	1.00[ASN][1000 genomes]
rs7779854	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7781557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790451	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7809047	1.00[CHB][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2761100	chr7:102335787-102481978	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv608057	chr7:102440184-102538515	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv608059	chr7:102470455-102504773	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17474893	POLR2J	cis	multi-tissue	Pritchard
rs17474893	CUX1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102454200-102484600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:102459800-102481800	Weak transcription	Brain Substantia Nigra	brain
3	chr7:102460400-102480800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:102460800-102480800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:102468000-102484600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:102468200-102481000	Weak transcription	Brain Germinal Matrix	brain
7	chr7:102470000-102490200	Weak transcription	Gastric	stomach
8	chr7:102470000-102516400	Weak transcription	Pancreas	Pancrea
9	chr7:102470200-102481800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:102470400-102481600	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:102470400-102482800	Weak transcription	Brain Anterior Caudate	brain
12	chr7:102470600-102481800	Weak transcription	Brain Angular Gyrus	brain
13	chr7:102470800-102484400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:102470800-102493200	Weak transcription	Primary T cells from cord blood	blood
15	chr7:102471800-102500000	Weak transcription	Left Ventricle	heart
16	chr7:102472000-102484800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:102476000-102480800	Weak transcription	GM12878-XiMat	blood
18	chr7:102477400-102482400	Weak transcription	Stomach Mucosa	stomach
19	chr7:102477800-102481800	Weak transcription	Hela-S3	cervix
20	chr7:102477800-102482200	Weak transcription	Psoas Muscle	Psoas
21	chr7:102477800-102500800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:102478000-102480800	Weak transcription	HSMM	muscle
23	chr7:102478000-102481000	Enhancers	HepG2	liver
24	chr7:102478000-102489200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:102478200-102480800	Weak transcription	HSMMtube	muscle
26	chr7:102478200-102481800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr7:102478200-102481800	Weak transcription	Fetal Stomach	stomach
28	chr7:102478200-102500000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:102478200-102500000	Weak transcription	Ovary	ovary
30	chr7:102478600-102480800	Weak transcription	Fetal Muscle Leg	muscle
31	chr7:102478600-102482000	Weak transcription	NHDF-Ad	bronchial
32	chr7:102478800-102481800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:102478800-102482200	Weak transcription	K562	blood
34	chr7:102478800-102482800	Weak transcription	Fetal Intestine Large	intestine
35	chr7:102478800-102489600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr7:102478800-102492600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:102479200-102480800	Weak transcription	Fetal Lung	lung
38	chr7:102480400-102481400	Enhancers	A549	lung

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