Variant report

Variant	rs13112866
Chromosome Location	chr4:102120454-102120455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102112038..102115219-chr4:102118263..102121528,3	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10004357	0.81[JPT][hapmap]
rs10005338	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10016669	0.81[JPT][hapmap]
rs10018021	0.86[EUR][1000 genomes]
rs10025780	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10030389	0.92[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs10050301	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10516471	0.92[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs11934140	0.84[CHB][hapmap]
rs11941610	0.86[CHB][hapmap]
rs13103902	0.86[EUR][1000 genomes]
rs13111186	0.85[EUR][1000 genomes]
rs13115754	0.80[CHB][hapmap]
rs13116679	0.80[CHB][hapmap]
rs13117949	0.80[CHB][hapmap]
rs13118966	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13123962	0.81[JPT][hapmap]
rs13125501	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13128841	0.92[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs13135924	0.85[EUR][1000 genomes]
rs13137393	0.80[CHB][hapmap]
rs13142024	0.92[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs1880943	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs2048072	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2063058	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs2135611	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2165505	0.81[JPT][hapmap]
rs2174680	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2583407	0.80[CHB][hapmap]
rs2695217	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs2695219	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs2850336	0.80[CHB][hapmap]
rs2850359	0.86[CHB][hapmap]
rs2850964	0.80[CHB][hapmap]
rs3789748	0.81[JPT][hapmap]
rs3804361	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804368	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804381	0.86[CHB][hapmap]
rs3804406	0.86[CHB][hapmap]
rs3804408	0.86[CHB][hapmap]
rs3804416	0.80[CHB][hapmap]
rs3811063	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[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]
rs3827770	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4590038	0.85[EUR][1000 genomes]
rs4698912	0.92[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4698913	0.85[EUR][1000 genomes]
rs4699106	0.85[EUR][1000 genomes]
rs4699116	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699127	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs713455	0.86[CHB][hapmap]
rs7677550	0.92[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs950177	0.89[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs958379	0.85[CHB][hapmap]
rs9884638	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995338	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13112866	CXXC4	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102105400-102126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:102106200-102121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:102107600-102126600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr4:102109200-102126200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:102109800-102122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:102111200-102122400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:102113200-102121000	Weak transcription	HSMM	muscle
8	chr4:102113200-102122400	Weak transcription	Aorta	Aorta
9	chr4:102113200-102124400	Weak transcription	Pancreas	Pancrea
10	chr4:102113400-102120800	Weak transcription	NH-A	brain
11	chr4:102113600-102120600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:102113600-102120800	Weak transcription	Right Ventricle	heart
13	chr4:102113600-102121400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:102113600-102122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:102113800-102120600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:102113800-102120800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:102113800-102121000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:102113800-102121000	Weak transcription	HMEC	breast
19	chr4:102113800-102122800	Weak transcription	Right Atrium	heart
20	chr4:102113800-102126200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:102113800-102127200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:102113800-102131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:102114000-102120600	Weak transcription	NHDF-Ad	bronchial
24	chr4:102114000-102121200	Weak transcription	Adipose Nuclei	Adipose
25	chr4:102114800-102121200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:102115400-102120800	Weak transcription	Osteobl	bone
27	chr4:102117000-102120800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:102117000-102121600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:102117200-102120600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:102117200-102120600	Weak transcription	NHLF	lung
31	chr4:102117200-102121200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:102117200-102121200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr4:102117200-102125800	Weak transcription	Dnd41	blood
34	chr4:102117200-102126200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr4:102117400-102121200	Weak transcription	NHEK	skin
36	chr4:102117600-102121400	Enhancers	Fetal Intestine Small	intestine
37	chr4:102117600-102123000	Enhancers	HepG2	liver
38	chr4:102117800-102121800	Enhancers	Liver	Liver
39	chr4:102117800-102124200	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr4:102118000-102132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:102118200-102121800	Enhancers	Colon Smooth Muscle	Colon
42	chr4:102118200-102126800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr4:102118800-102126200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr4:102119200-102121600	Enhancers	Fetal Intestine Large	intestine
45	chr4:102119200-102122200	Enhancers	Brain Anterior Caudate	brain
46	chr4:102119400-102120600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:102119400-102120600	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr4:102119400-102121400	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr4:102119400-102121800	Enhancers	Primary B cells from cord blood	blood
50	chr4:102119400-102122800	Enhancers	Primary T helper cells PMA-I stimulated	--

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