Variant report

Variant	rs11407
Chromosome Location	chr19:44085827-44085828
allele	A/G
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	JUND	chr19:44085777-44085883	K562	blood:	n/a	n/a
2	MYC	chr19:44085699-44085960	K562	blood:	n/a	n/a
3	ATF1	chr19:44085608-44086104	K562	blood:	n/a	n/a
4	JUND	chr19:44083900-44086327	SK-N-SH	brain:	n/a	chr19:44084081-44084088
5	BHLHE40	chr19:44085658-44086026	K562	blood:	n/a	n/a
6	RCOR1	chr19:44085694-44086161	K562	blood:	n/a	n/a
7	MAX	chr19:44085634-44086076	K562	blood:	n/a	n/a
8	USF1	chr19:44085724-44085907	K562	blood:	n/a	n/a
9	POLR2A	chr19:44085192-44085975	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44082767..44086072-chr19:44097414..44100193,3	MCF-7	breast:
2	chr19:44080117..44083864-chr19:44085399..44088767,4	K562	blood:

Variant related genes	Relation type
XRCC1	TF binding region
ENSG00000167378	Chromatin interaction
ENSG00000073050	Chromatin interaction
ENSG00000234465	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2021092	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs25484	1.00[ASW][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2599442	0.90[ASW][hapmap];0.90[YRI][hapmap]
rs2599459	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2599464	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682552	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682560	1.00[ASW][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682562	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682587	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
rs2682588	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes]
rs2854495	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2854496	1.00[ASW][hapmap];0.80[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2854497	0.81[YRI][hapmap]
rs2854498	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2854502	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2854505	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2854510	0.82[ASW][hapmap];0.80[CEU][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs304729	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs304730	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3213283	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3213285	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3213289	0.85[EUR][1000 genomes]
rs3213332	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3213370	0.87[EUR][1000 genomes]
rs939460	1.00[ASW][hapmap];0.80[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv1063149	chr19:44059081-44087583	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11407	ZNF575	cis	Nerve Tibial	GTEx
rs11407	SIGLEC14	cis	parietal	SCAN
rs11407	ZNF575	cis	Adipose Subcutaneous	GTEx
rs11407	BCAT2	cis	cerebellum	SCAN
rs11407	PHLDB3	cis	normal skin	skin_eQTL
rs11407	ZNF575	cis	Skin Sun Exposed Lower leg	GTEx
rs11407	NANOS2	cis	parietal	SCAN
rs11407	SLC8A2	cis	cerebellum	SCAN
rs11407	XRCC1	cis	lymphoblastoid	seeQTL
rs11407	SNRPD2	cis	parietal	SCAN
rs11407	ZNF575	cis	Artery Tibial	GTEx
rs11407	PHLDB3	cis	lesional skin	skin_eQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44079800-44098200	Weak transcription	Small Intestine	intestine
2	chr19:44080400-44090200	Weak transcription	HSMM	muscle
3	chr19:44080600-44090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:44080600-44095600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:44080800-44088400	Weak transcription	A549	lung
6	chr19:44081400-44090200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:44081400-44090200	Weak transcription	NHEK	skin
8	chr19:44081600-44090600	Weak transcription	HMEC	breast
9	chr19:44083000-44087800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:44084400-44086800	Enhancers	Spleen	Spleen
11	chr19:44084600-44086200	Enhancers	Fetal Heart	heart
12	chr19:44084600-44086200	Enhancers	Placenta	Placenta
13	chr19:44084600-44086400	Enhancers	K562	blood
14	chr19:44084600-44088200	Weak transcription	Liver	Liver
15	chr19:44084600-44088400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr19:44084600-44090200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:44084600-44090200	Enhancers	Primary B cells from cord blood	blood
18	chr19:44084600-44090200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:44084600-44090400	Enhancers	Primary B cells from peripheral blood	blood
20	chr19:44084600-44093000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:44084600-44093000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:44084600-44093000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:44084600-44093000	Weak transcription	HUVEC	blood vessel
24	chr19:44084600-44093800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:44084600-44094000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr19:44084600-44096800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:44084600-44098200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:44084800-44086000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr19:44084800-44089800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:44084800-44095400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr19:44084800-44097400	Weak transcription	NH-A	brain
32	chr19:44085000-44086000	Enhancers	Thymus	Thymus
33	chr19:44085000-44086200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr19:44085000-44086200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:44085000-44086200	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr19:44085000-44087200	Enhancers	Primary hematopoietic stem cells	blood
37	chr19:44085000-44089800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:44085000-44095600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:44085000-44095600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:44085200-44086000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr19:44085200-44086000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr19:44085200-44086000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:44085200-44086000	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr19:44085200-44086000	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr19:44085200-44086000	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr19:44085200-44086000	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr19:44085200-44086000	Flanking Active TSS	Fetal Lung	lung
48	chr19:44085200-44086200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:44085200-44086200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr19:44085200-44086200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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