Variant report

Variant	rs10517204
Chromosome Location	chr4:48036711-48036712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48017908..48020404-chr4:48035572..48037136,2	MCF-7	breast:
2	chr4:48034068..48036913-chr4:48142592..48144853,2	MCF-7	breast:
3	chr4:48035341..48036908-chr4:48088867..48089881,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163293	Chromatin interaction
ENSG00000198515	Chromatin interaction
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10002500	0.93[ASW][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.86[YRI][hapmap]
rs10805163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938520	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733288	0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12645245	0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13107767	0.87[JPT][hapmap]
rs1371729	0.80[ASW][hapmap];0.82[YRI][hapmap]
rs1396051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466997	0.83[JPT][hapmap]
rs178650	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2352470	0.81[YRI][hapmap]
rs2661513	0.90[YRI][hapmap]
rs28578328	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3113881	0.86[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs321621	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs321623	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs321633	0.89[CEU][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3805187	0.83[JPT][hapmap]
rs3950558	0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4694880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4695326	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4695332	0.87[JPT][hapmap]
rs6850603	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6858440	0.80[ASW][hapmap]
rs7685636	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995122	0.86[ASW][hapmap];0.82[YRI][hapmap]
rs9996535	0.83[JPT][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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10517204	NFXL1	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
3	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
4	chr4:48024600-48043600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:48026800-48045400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:48028200-48040800	Weak transcription	Gastric	stomach
7	chr4:48028200-48042600	Weak transcription	Placenta	Placenta
8	chr4:48028400-48037400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:48031600-48041800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:48032800-48045000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:48033000-48037600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:48033000-48037600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:48033000-48037800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:48033000-48037800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:48033000-48045000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:48034000-48038600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:48034200-48037600	Enhancers	GM12878-XiMat	blood
18	chr4:48034200-48049600	Weak transcription	Pancreas	Pancrea
19	chr4:48034400-48039400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:48034800-48039200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:48034800-48041600	Strong transcription	HMEC	breast
22	chr4:48035000-48038000	Strong transcription	NHEK	skin
23	chr4:48035000-48039000	Weak transcription	Hela-S3	cervix
24	chr4:48035200-48037800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:48035200-48038200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:48035800-48036800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:48035800-48040200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:48036000-48036800	Weak transcription	Liver	Liver
29	chr4:48036000-48038400	Weak transcription	Fetal Heart	heart
30	chr4:48036000-48040400	Enhancers	Primary B cells from peripheral blood	blood
31	chr4:48036200-48036800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:48036200-48037800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:48036200-48040000	Weak transcription	HepG2	liver
34	chr4:48036200-48041000	Enhancers	Primary B cells from cord blood	blood
35	chr4:48036400-48037000	Weak transcription	Fetal Intestine Large	intestine
36	chr4:48036400-48038000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:48036400-48038400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:48036400-48046400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:48036600-48038200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr4:48036600-48040400	Weak transcription	Fetal Intestine Small	intestine

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