Variant report

Variant	rs3093907
Chromosome Location	chr14:20819729-20819730
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	chr14:20818052..20820048-chr14:20820385..20822938,2	K562	blood:
2	chr14:20810396..20814723-chr14:20817267..20820679,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259001	Chromatin interaction
ENSG00000129484	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10129957	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs10147163	0.82[CEU][hapmap]
rs10148359	0.82[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap]
rs10873395	0.89[CHD][hapmap]
rs11622655	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs12891805	0.87[ASN][1000 genomes]
rs1713413	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1713414	0.83[EUR][1000 genomes]
rs1713415	0.83[EUR][1000 genomes]
rs1713430	0.84[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs1760912	0.83[EUR][1000 genomes]
rs1760918	0.83[EUR][1000 genomes]
rs1760919	0.83[EUR][1000 genomes]
rs1760923	0.81[EUR][1000 genomes]
rs1889363	0.84[MEX][hapmap];0.90[TSI][hapmap]
rs2297616	0.84[ASW][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs2297617	0.84[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2318864	0.87[CHD][hapmap]
rs2319190	0.82[EUR][1000 genomes]
rs2678682	0.83[EUR][1000 genomes]
rs2678683	0.83[EUR][1000 genomes]
rs2700	0.90[GIH][hapmap]
rs3093882	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3093890	0.84[ASW][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs3093897	0.92[ASN][1000 genomes]
rs3093900	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093902	0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs3093904	0.92[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs3093909	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093933	0.93[GIH][hapmap];0.94[MEX][hapmap]
rs3093939	0.82[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap]
rs3093942	0.80[JPT][hapmap];0.94[MEX][hapmap]
rs3742945	0.87[CHD][hapmap]
rs4981150	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4981153	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4981158	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs4981983	0.86[ASN][1000 genomes]
rs6575135	0.84[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs7155699	0.84[ASW][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs7159947	0.84[CEU][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs7161611	0.82[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap]
rs8009242	0.84[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs8014147	0.87[ASN][1000 genomes]
rs8022565	0.84[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs878157	0.82[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs884368	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9323870	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats 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	203 gene(s)	inside rSNPs	diseases
3	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
4	nsv541974	chr14:20517485-20901811	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
5	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription 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	71 gene(s)	inside rSNPs	diseases
6	nsv534131	chr14:20757405-20886235	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	esv21015	chr14:20800765-21257878	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3093907	CCNB1IP1	cis	parietal	SCAN
rs3093907	PARP2	cis	parietal	SCAN
rs3093907	RPPH1	cis	multi-tissue	Pritchard
rs3093907	TTC5	cis	cerebellum	SCAN
rs3093907	PRMT5	cis	parietal	SCAN
rs3093907	PARP2	cis	cerebellum	SCAN
rs3093907	CCNB1IP1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20812000-20820600	Weak transcription	Spleen	Spleen
2	chr14:20812000-20822600	Weak transcription	Gastric	stomach
3	chr14:20812200-20822600	Weak transcription	Pancreas	Pancrea
4	chr14:20812200-20824000	Weak transcription	Aorta	Aorta
5	chr14:20812200-20825400	Weak transcription	Esophagus	oesophagus
6	chr14:20812400-20820400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:20812400-20824400	Weak transcription	Stomach Mucosa	stomach
8	chr14:20812400-20880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr14:20812600-20820200	Weak transcription	Colonic Mucosa	Colon
10	chr14:20812600-20820600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr14:20812600-20820600	Weak transcription	Psoas Muscle	Psoas
12	chr14:20812600-20820600	Weak transcription	Right Ventricle	heart
13	chr14:20812600-20820800	Weak transcription	NHDF-Ad	bronchial
14	chr14:20812600-20822200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr14:20812600-20824400	Weak transcription	Fetal Heart	heart
16	chr14:20812600-20831800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr14:20812600-20834600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr14:20812600-20841000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr14:20812600-20845600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr14:20812800-20820600	Weak transcription	NHLF	lung
21	chr14:20812800-20824000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr14:20813000-20827000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr14:20813000-20827800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr14:20813000-20827800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr14:20813000-20830800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:20813200-20819800	Strong transcription	Fetal Kidney	kidney
27	chr14:20813200-20820800	Weak transcription	Fetal Brain Male	brain
28	chr14:20813200-20821600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr14:20813200-20824400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr14:20813200-20824400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr14:20813200-20825800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr14:20813200-20825800	Strong transcription	Fetal Stomach	stomach
33	chr14:20813200-20826200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr14:20813200-20826600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr14:20813200-20826800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr14:20813200-20827000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr14:20813200-20827000	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr14:20813200-20827400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr14:20813200-20827600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr14:20813200-20827600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr14:20813200-20827800	Strong transcription	Fetal Intestine Large	intestine
42	chr14:20813200-20827800	Strong transcription	Placenta	Placenta
43	chr14:20813200-20828000	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr14:20813200-20828400	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr14:20813200-20829400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr14:20813200-20831600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr14:20813200-20869200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr14:20813400-20820600	Strong transcription	A549	lung
49	chr14:20813400-20826000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr14:20813400-20826400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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