Variant report

Variant	rs962539
Chromosome Location	chr14:78329737-78329738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78327949..78329774-chr14:78457367..78458415,8	MCF-7	breast:
2	chr14:78327978..78330671-chr14:78388681..78391406,2	K562	blood:
3	chr14:78327427..78330329-chr14:78335652..78337700,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000063761	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10130790	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs10146144	0.82[ASN][1000 genomes]
rs1107991	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11159290	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs11159291	0.95[CHB][hapmap]
rs11159294	0.91[CHB][hapmap]
rs11159298	0.95[CHB][hapmap]
rs11159300	0.86[CEU][hapmap];0.96[CHB][hapmap];0.83[JPT][hapmap]
rs11159301	0.86[CEU][hapmap];0.96[CHB][hapmap];0.83[JPT][hapmap]
rs11159302	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs11159303	0.80[AMR][1000 genomes]
rs11159306	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11622297	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs11628049	0.91[CHB][hapmap]
rs12587361	0.86[CEU][hapmap];0.96[CHB][hapmap];0.82[JPT][hapmap]
rs12878904	0.91[CHB][hapmap]
rs12879726	0.87[CHB][hapmap]
rs12884153	0.87[CHB][hapmap]
rs12893815	0.84[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2003600	0.87[CHB][hapmap]
rs2017927	0.84[CHB][hapmap]
rs2052444	0.91[CHB][hapmap]
rs2080814	0.89[ASN][1000 genomes]
rs2080815	0.96[CHB][hapmap]
rs2080816	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2080817	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2098583	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2098584	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2287648	0.95[CHB][hapmap]
rs2287650	0.83[CHB][hapmap]
rs2364739	0.88[ASN][1000 genomes]
rs2364741	0.89[ASN][1000 genomes]
rs2364743	0.86[CEU][hapmap];0.96[CHB][hapmap];0.83[JPT][hapmap]
rs2364745	0.80[ASN][1000 genomes]
rs2364842	0.87[CHB][hapmap]
rs2886167	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs2886168	0.91[CHB][hapmap]
rs3783962	0.82[CEU][hapmap];0.96[CHB][hapmap];0.82[JPT][hapmap]
rs3783966	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3783968	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap]
rs3783969	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3783971	0.80[ASN][1000 genomes]
rs3783974	0.88[CHB][hapmap]
rs3825691	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs3825692	0.88[ASN][1000 genomes]
rs4359362	0.87[CHB][hapmap]
rs4371094	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4393507	0.87[CHB][hapmap]
rs4448861	0.83[CHB][hapmap]
rs4899677	0.91[CHB][hapmap]
rs4899678	0.95[CHB][hapmap]
rs4899679	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs4903654	0.87[CHB][hapmap]
rs4903655	0.83[CHB][hapmap]
rs4903656	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4903658	0.86[CEU][hapmap];0.96[CHB][hapmap];0.83[JPT][hapmap]
rs4903660	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4903661	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs4903662	0.88[CHB][hapmap];0.92[ASN][1000 genomes]
rs4903663	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4903664	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4903666	0.84[CHB][hapmap]
rs4903667	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs6574406	0.80[ASN][1000 genomes]
rs6574408	0.82[ASN][1000 genomes]
rs7145309	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs7145567	0.83[CHB][hapmap]
rs7147735	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs7149884	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs719049	0.87[CHB][hapmap]
rs724263	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs726538	0.91[CHB][hapmap]
rs734654	0.83[CHB][hapmap]
rs741573	0.86[CEU][hapmap];0.96[CHB][hapmap];0.83[JPT][hapmap]
rs741574	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs741575	0.89[CEU][hapmap];0.91[CHB][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7493386	0.90[CHB][hapmap]
rs8004053	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8010212	0.85[ASN][1000 genomes]
rs8014296	0.95[CHB][hapmap]
rs8018674	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs8019539	0.90[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8022985	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs874025	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs877561	0.85[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78293400-78331800	Weak transcription	Pancreas	Pancrea
2	chr14:78297600-78336600	Weak transcription	Left Ventricle	heart
3	chr14:78297800-78353600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr14:78301400-78342200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr14:78302200-78331000	Weak transcription	Liver	Liver
6	chr14:78306000-78331800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr14:78306000-78356400	Weak transcription	Thymus	Thymus
8	chr14:78306600-78330400	Weak transcription	Dnd41	blood
9	chr14:78310000-78339400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr14:78310400-78345000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr14:78314200-78348400	Weak transcription	Colon Smooth Muscle	Colon
12	chr14:78320800-78342200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr14:78321400-78342800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr14:78321800-78335400	Weak transcription	Psoas Muscle	Psoas
15	chr14:78321800-78348400	Weak transcription	Placenta	Placenta
16	chr14:78322000-78342000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr14:78322000-78342600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr14:78322200-78353400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr14:78322800-78331600	Enhancers	K562	blood
20	chr14:78323400-78339600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr14:78323600-78330600	Weak transcription	Aorta	Aorta
22	chr14:78323600-78331600	Weak transcription	Primary B cells from cord blood	blood
23	chr14:78324000-78353600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr14:78324200-78354800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr14:78324400-78339800	Weak transcription	Ovary	ovary
26	chr14:78324800-78330400	Weak transcription	Stomach Mucosa	stomach
27	chr14:78325000-78332400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr14:78325000-78345000	Weak transcription	Brain Angular Gyrus	brain
29	chr14:78325800-78330800	Weak transcription	Spleen	Spleen
30	chr14:78326400-78339800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr14:78326400-78342000	Weak transcription	Adipose Nuclei	Adipose
32	chr14:78326600-78352800	Weak transcription	Esophagus	oesophagus
33	chr14:78327000-78338000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr14:78327000-78339400	Weak transcription	Fetal Muscle Leg	muscle
35	chr14:78327000-78342000	Weak transcription	Lung	lung
36	chr14:78327200-78330600	Weak transcription	Gastric	stomach
37	chr14:78327200-78348600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr14:78327400-78331800	Weak transcription	Fetal Stomach	stomach
39	chr14:78327800-78400600	Weak transcription	Colonic Mucosa	Colon
40	chr14:78328000-78331800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr14:78328000-78338200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr14:78328000-78353400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr14:78328200-78330400	Weak transcription	Primary T cells from cord blood	blood
44	chr14:78328200-78330400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr14:78329000-78345000	Weak transcription	Brain Substantia Nigra	brain
46	chr14:78329000-78345800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr14:78329000-78347600	Weak transcription	Brain Anterior Caudate	brain
48	chr14:78329000-78348400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr14:78329200-78330200	Weak transcription	Fetal Intestine Small	intestine
50	chr14:78329200-78345400	Weak transcription	Right Ventricle	heart

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