Variant report

Variant	rs11160341
Chromosome Location	chr14:97013249-97013250
allele	C/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	POLR2A	chr14:97013186-97013269	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:97010400..97013410-chr14:97024824..97026785,3	K562	blood:
2	chr14:97011141..97013270-chr14:97015044..97017205,2	K562	blood:
3	chr14:96985630..96987652-chr14:97013134..97015914,2	MCF-7	breast:
4	chr14:97007480..97011210-chr14:97011511..97014615,3	K562	blood:

Variant related genes	Relation type
PAPOLA	TF binding region
ENSG00000090060	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10136266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10136277	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10139164	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10140247	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10143834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10144704	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10145194	0.83[JPT][hapmap]
rs10467873	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11160344	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11621566	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11621778	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11623142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11625090	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11627288	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11848720	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11848778	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12147439	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12147717	0.83[JPT][hapmap]
rs12586789	0.83[JPT][hapmap]
rs13329034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13379390	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1484251	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17094149	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28600893	0.83[JPT][hapmap];0.85[TSI][hapmap]
rs28718054	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28738720	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2887550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809425	0.83[JPT][hapmap]
rs4514608	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56184178	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56960368	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58112821	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60920648	0.91[EUR][1000 genomes]
rs61435932	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61570427	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66881740	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7142226	0.83[JPT][hapmap]
rs7142806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7146883	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7160148	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8013517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs965950	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042409	chr14:96832303-97115668	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv542178	chr14:96832303-97115668	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3442210	chr14:96878392-97038700	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv1802671	chr14:96942352-97035680	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1052499	chr14:96974524-97034805	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	esv1793036	chr14:96983291-97023059	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1048302	chr14:97000845-97250538	Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv1791939	chr14:97001679-97027747	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1041078	chr14:97001679-97279220	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv1050075	chr14:97004951-97279220	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:96978000-97019400	Weak transcription	Aorta	Aorta
2	chr14:96979600-97022400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:96979800-97019200	Weak transcription	Small Intestine	intestine
4	chr14:96980800-97020600	Weak transcription	Stomach Mucosa	stomach
5	chr14:96982000-97031400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr14:96984800-97020800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr14:96984800-97039400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr14:96989000-97018800	Weak transcription	Lung	lung
9	chr14:96989200-97018600	Weak transcription	Brain Substantia Nigra	brain
10	chr14:96991400-97022400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr14:96993000-97018800	Weak transcription	Gastric	stomach
12	chr14:96993000-97018800	Weak transcription	Pancreas	Pancrea
13	chr14:96993000-97018800	Weak transcription	Spleen	Spleen
14	chr14:96993200-97018800	Weak transcription	Esophagus	oesophagus
15	chr14:96993600-97017400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr14:96993600-97018800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr14:96993600-97018800	Weak transcription	Ovary	ovary
18	chr14:96994000-97018800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr14:96994400-97018800	Weak transcription	Colonic Mucosa	Colon
20	chr14:96997800-97015600	Weak transcription	Fetal Intestine Small	intestine
21	chr14:96997800-97015800	Weak transcription	Fetal Stomach	stomach
22	chr14:96997800-97016200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:96997800-97018800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr14:96999000-97016200	Weak transcription	Thymus	Thymus
25	chr14:96999200-97013800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr14:96999200-97018800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr14:96999200-97018800	Weak transcription	Psoas Muscle	Psoas
28	chr14:96999200-97020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr14:96999200-97022200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr14:96999400-97040600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr14:96999800-97013800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr14:97001000-97017200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr14:97001000-97018600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr14:97001000-97018800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr14:97001200-97018600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr14:97001800-97019200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr14:97002400-97019600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr14:97002600-97033800	Weak transcription	Fetal Brain Male	brain
39	chr14:97003000-97018000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr14:97003800-97018800	Weak transcription	Colon Smooth Muscle	Colon
41	chr14:97003800-97019600	Weak transcription	Brain Hippocampus Middle	brain
42	chr14:97005400-97015600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr14:97006400-97040400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr14:97006600-97024400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr14:97007600-97035200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr14:97007600-97036000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr14:97007800-97034800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr14:97008000-97019600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr14:97008000-97036000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr14:97008200-97017600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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