Variant report

Variant	rs17010857
Chromosome Location	chr4:86695978-86695979
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr4:86695626-86696082	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr4:86695584-86696064	MCF-7	breast:	n/a	n/a
3	TCF7L2	chr4:86695230-86696114	HEK293	kidney:	n/a	chr4:86695371-86695380
4	KAP1	chr4:86695211-86696020	HEK293	kidney:	n/a	n/a
5	GATA3	chr4:86695676-86696051	MCF-7	breast:	n/a	chr4:86695883-86695893 chr4:86695687-86695697

Variant related genes	Relation type
ARHGAP24	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1014642	0.82[EUR][1000 genomes]
rs11097071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11945319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498959	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12505724	0.83[EUR][1000 genomes]
rs12506038	0.82[EUR][1000 genomes]
rs12507198	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12508919	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12509904	0.84[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap]
rs12510148	0.83[EUR][1000 genomes]
rs13102863	0.82[EUR][1000 genomes]
rs13106553	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13108523	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs13110928	0.82[EUR][1000 genomes]
rs13127367	0.82[EUR][1000 genomes]
rs13134382	0.88[YRI][hapmap]
rs13136153	0.83[EUR][1000 genomes]
rs13137575	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13139248	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17010851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17010863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1966862	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2004613	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34056429	0.82[EUR][1000 genomes]
rs34820504	0.82[EUR][1000 genomes]
rs35472747	0.83[EUR][1000 genomes]
rs3889735	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4693127	0.91[EUR][1000 genomes]
rs4693734	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4693735	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4693736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58146546	0.82[EUR][1000 genomes]
rs6813860	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs71599423	0.82[EUR][1000 genomes]
rs7676486	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs900204	0.94[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription 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	5 gene(s)	inside rSNPs	diseases
4	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv879517	chr4:86677107-86739805	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17010857	MRPS18C	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86663400-86699800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:86676800-86697800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr4:86682000-86697000	Weak transcription	Psoas Muscle	Psoas
4	chr4:86683200-86699000	Weak transcription	Primary B cells from cord blood	blood
5	chr4:86684800-86705600	Weak transcription	Small Intestine	intestine
6	chr4:86688600-86696800	Weak transcription	Fetal Kidney	kidney
7	chr4:86693800-86697000	Weak transcription	Osteobl	bone
8	chr4:86694000-86697000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:86694000-86697200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr4:86694400-86696000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr4:86694400-86696200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr4:86694400-86696400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:86694400-86696400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr4:86694400-86697400	Enhancers	HUVEC	blood vessel
15	chr4:86694600-86696600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr4:86694600-86697000	Weak transcription	NHDF-Ad	bronchial
17	chr4:86694800-86696400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr4:86694800-86697600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:86695000-86696000	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr4:86695000-86696200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr4:86695000-86697200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:86695200-86696000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr4:86695200-86696000	Enhancers	NHEK	skin
24	chr4:86695400-86696000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:86695400-86696000	Enhancers	Stomach Mucosa	stomach
26	chr4:86695400-86696600	Weak transcription	Spleen	Spleen
27	chr4:86695400-86699200	Weak transcription	Gastric	stomach
28	chr4:86695400-86708200	Weak transcription	Pancreas	Pancrea
29	chr4:86695600-86696800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:86695600-86696800	Weak transcription	Fetal Heart	heart
31	chr4:86695600-86697400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:86695600-86697400	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:86695600-86697600	Weak transcription	Esophagus	oesophagus
34	chr4:86695600-86699800	Weak transcription	Right Ventricle	heart
35	chr4:86695800-86696000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:86695800-86696000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:86695800-86696200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
38	chr4:86695800-86697400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:86695800-86697400	Weak transcription	HMEC	breast

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