Variant report

Variant	rs4902622
Chromosome Location	chr14:39888772-39888773
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39882950..39886541-chr14:39887581..39892204,4	MCF-7	breast:
2	chr14:39888039..39890423-chr14:39893808..39896011,2	MCF-7	breast:
3	chr14:39887184..39890386-chr14:39899843..39902826,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165355	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10131617	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs10133417	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs10134365	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs10137352	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs10137905	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.80[TSI][hapmap]
rs10151659	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs10162550	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10872920	0.81[JPT][hapmap]
rs11157053	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11157058	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11157067	0.87[AFR][1000 genomes]
rs11620695	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs11621330	0.81[JPT][hapmap]
rs11626679	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs11627580	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs11847057	0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12232110	0.96[ASN][1000 genomes]
rs12434140	0.81[JPT][hapmap]
rs12587625	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12587713	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs12588110	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12588175	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12588483	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12589427	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12590172	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12880644	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12882250	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12883652	0.80[ASN][1000 genomes]
rs12884747	0.96[AFR][1000 genomes]
rs12886769	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12894855	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12896502	0.91[CHB][hapmap]
rs12897960	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1594842	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17109021	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs17109028	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs17109073	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs17109300	1.00[ASW][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs17109328	0.95[AFR][1000 genomes]
rs1897792	0.81[JPT][hapmap]
rs1950329	0.96[AFR][1000 genomes]
rs1950334	0.94[AFR][1000 genomes]
rs1950336	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1950338	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1950952	0.81[JPT][hapmap]
rs1955718	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2038278	0.80[ASN][1000 genomes]
rs2057137	0.91[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap]
rs2057138	0.91[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs2082635	0.81[JPT][hapmap]
rs2207291	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274395	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2274396	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs2274399	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2415543	0.85[ASW][hapmap]
rs2415549	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2415550	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899888	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2899889	0.87[ASN][1000 genomes]
rs34432449	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34589600	0.81[ASN][1000 genomes]
rs34649642	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34687394	0.96[AFR][1000 genomes]
rs34894621	0.81[ASN][1000 genomes]
rs35115885	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35459433	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35553183	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35643160	0.96[AFR][1000 genomes]
rs35693868	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35876588	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35923045	0.95[AFR][1000 genomes]
rs36010374	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814860	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4899245	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4899277	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4899278	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4899291	0.95[AFR][1000 genomes]
rs4902569	0.85[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4902570	0.85[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4902598	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902599	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902636	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4902637	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4902648	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902665	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902676	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902692	0.91[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs56046902	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56375627	0.81[ASN][1000 genomes]
rs6571919	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs67439322	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs67963654	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs71407788	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71407789	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7140983	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7143646	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7145821	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7148150	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7148377	0.87[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7152341	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7152935	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7153413	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7158709	0.96[AFR][1000 genomes]
rs7161403	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs718364	0.87[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs719455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs72675487	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8003397	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8003621	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8004716	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs8006123	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8006321	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8018717	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs8020250	0.95[AFR][1000 genomes]
rs910370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs910371	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332387	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs956109	0.83[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4902622	CTAGE5	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39863400-39891600	Weak transcription	Small Intestine	intestine
2	chr14:39864600-39898800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr14:39865000-39891200	Weak transcription	Psoas Muscle	Psoas
4	chr14:39865000-39898200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr14:39869000-39895600	Weak transcription	Hela-S3	cervix
6	chr14:39882200-39895400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr14:39885200-39891400	Weak transcription	Gastric	stomach
8	chr14:39886000-39890800	Weak transcription	Fetal Brain Male	brain
9	chr14:39886000-39895600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:39886200-39890600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr14:39886200-39895600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr14:39886400-39892600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr14:39886400-39895600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr14:39886600-39888800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr14:39886600-39889000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr14:39886600-39889600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:39886600-39889600	Weak transcription	Left Ventricle	heart
18	chr14:39886600-39890200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr14:39886600-39890200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr14:39886600-39890200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr14:39886600-39890800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr14:39886600-39890800	Weak transcription	Brain Angular Gyrus	brain
23	chr14:39886600-39891200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr14:39886600-39891200	Weak transcription	Lung	lung
25	chr14:39886600-39891200	Weak transcription	Ovary	ovary
26	chr14:39886600-39891200	Weak transcription	Right Ventricle	heart
27	chr14:39886600-39891400	Weak transcription	Aorta	Aorta
28	chr14:39886600-39891800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr14:39886600-39894000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr14:39886600-39894400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr14:39886600-39895600	Weak transcription	Fetal Lung	lung
32	chr14:39886600-39895800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr14:39886600-39895800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr14:39886600-39898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr14:39886600-39900000	Weak transcription	Esophagus	oesophagus
36	chr14:39886600-39900000	Weak transcription	Pancreas	Pancrea
37	chr14:39886800-39889800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr14:39886800-39890200	Weak transcription	Primary T cells from cord blood	blood
39	chr14:39886800-39890200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr14:39886800-39891200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr14:39886800-39892600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr14:39886800-39895600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr14:39886800-39895600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr14:39886800-39895600	Weak transcription	HepG2	liver
45	chr14:39886800-39895800	Weak transcription	Brain Anterior Caudate	brain
46	chr14:39886800-39895800	Weak transcription	Fetal Thymus	thymus
47	chr14:39886800-39895800	Weak transcription	Thymus	Thymus
48	chr14:39886800-39899200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr14:39886800-39899600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr14:39887000-39895800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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