Variant report

Variant	rs11621330
Chromosome Location	chr14:39741978-39741979
allele	G/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	chr14:39741845-39741988	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:39736982..39739247-chr14:39739513..39742286,3	K562	blood:
2	chr14:39734713..39738415-chr14:39740999..39745819,7	MCF-7	breast:
3	chr14:39733456..39736427-chr14:39738159..39742075,4	K562	blood:
4	chr14:39733186..39738068-chr14:39738751..39742738,6	MCF-7	breast:

Variant related genes	Relation type
CTAGE5	TF binding region
ENSG00000258940	Chromatin interaction
ENSG00000258941	Chromatin interaction
ENSG00000150527	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10131617	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10133417	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10134365	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10137352	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10137905	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10138869	0.86[JPT][hapmap]
rs10151659	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10162550	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1040810	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10872920	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs11157053	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11157054	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11157058	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11620695	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11621264	0.83[ASN][1000 genomes]
rs11626679	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11627580	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12432397	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12434140	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12587713	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12588728	0.84[ASN][1000 genomes]
rs12892482	0.83[ASN][1000 genomes]
rs12894855	0.86[JPT][hapmap]
rs1570132	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1594842	0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17109021	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs17109028	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs17109073	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1897792	0.91[JPT][hapmap]
rs1950952	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1998194	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2082635	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2274395	0.81[JPT][hapmap]
rs2274396	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2274399	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs2415545	0.81[ASW][hapmap]
rs28464771	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28626340	0.84[ASN][1000 genomes]
rs35065854	0.85[ASN][1000 genomes]
rs35184650	0.88[ASN][1000 genomes]
rs35201135	0.87[ASN][1000 genomes]
rs3814860	0.81[JPT][hapmap]
rs4902470	0.81[EUR][1000 genomes]
rs4902528	0.94[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs4902569	0.86[JPT][hapmap]
rs4902570	0.86[JPT][hapmap]
rs4902622	0.81[JPT][hapmap]
rs6571919	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7140164	0.86[JPT][hapmap]
rs7143646	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7148150	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7148377	0.82[JPT][hapmap]
rs7150735	0.81[ASN][1000 genomes]
rs7152341	0.81[JPT][hapmap]
rs7153482	0.86[JPT][hapmap]
rs718364	0.82[JPT][hapmap]
rs8004348	0.84[ASN][1000 genomes]
rs8004716	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs8006321	0.81[JPT][hapmap]
rs8011173	0.81[ASW][hapmap]
rs8018717	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8019328	0.81[ASW][hapmap]
rs956109	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][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	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
3	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11621330	CTAGE5	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39737000-39751800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:39737800-39748800	Weak transcription	Right Ventricle	heart
3	chr14:39737800-39750800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:39737800-39763800	Weak transcription	Gastric	stomach
5	chr14:39738000-39742400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr14:39738000-39742600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr14:39738000-39744400	Weak transcription	Right Atrium	heart
8	chr14:39738000-39748800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:39738000-39750600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr14:39738000-39752000	Weak transcription	Stomach Mucosa	stomach
11	chr14:39738000-39763800	Weak transcription	HSMM	muscle
12	chr14:39738200-39742000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr14:39738200-39745000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr14:39738200-39747000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr14:39738200-39748800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr14:39738200-39748800	Weak transcription	Fetal Kidney	kidney
17	chr14:39738200-39748800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr14:39738200-39748800	Weak transcription	Osteobl	bone
19	chr14:39738200-39751800	Weak transcription	Colonic Mucosa	Colon
20	chr14:39738200-39751800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr14:39738200-39759200	Weak transcription	NH-A	brain
22	chr14:39738200-39763800	Weak transcription	Brain Angular Gyrus	brain
23	chr14:39738200-39763800	Weak transcription	HSMMtube	muscle
24	chr14:39738200-39766200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:39738200-39813800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:39738600-39763800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr14:39738800-39747800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr14:39738800-39748800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr14:39738800-39748800	Weak transcription	Adipose Nuclei	Adipose
30	chr14:39738800-39748800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr14:39738800-39748800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr14:39738800-39764800	Weak transcription	NHDF-Ad	bronchial
33	chr14:39739000-39746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr14:39739000-39747200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr14:39739000-39748800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr14:39739000-39751800	Weak transcription	Brain Anterior Caudate	brain
37	chr14:39739200-39743800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr14:39739200-39747600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr14:39739200-39748800	Weak transcription	Brain Hippocampus Middle	brain
40	chr14:39739200-39748800	Weak transcription	HUVEC	blood vessel
41	chr14:39739200-39764000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr14:39739400-39745200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr14:39739400-39746400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr14:39739400-39747200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr14:39739400-39748800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr14:39739400-39749200	Weak transcription	Small Intestine	intestine
47	chr14:39739400-39758200	Weak transcription	NHEK	skin
48	chr14:39739800-39747000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr14:39739800-39763400	Weak transcription	Lung	lung
50	chr14:39739800-39766400	Weak transcription	Aorta	Aorta

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