Variant report

Variant	rs2414116
Chromosome Location	chr15:52017345-52017346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52010154..52013648-chr15:52016687..52020314,4	MCF-7	breast:
2	chr15:52015204..52021746-chr15:52024939..52031385,17	MCF-7	breast:
3	chr15:52013040..52016397-chr15:52016962..52020800,6	K562	blood:
4	chr15:52016515..52018648-chr15:52040542..52043046,2	MCF-7	breast:
5	chr15:52014160..52016391-chr15:52017218..52019564,2	MCF-7	breast:
6	chr15:52015670..52018450-chr15:52021031..52024231,3	K562	blood:

Variant related genes	Relation type
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1035737	0.81[GIH][hapmap]
rs10775145	0.89[GIH][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap]
rs11070864	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11070865	0.85[GIH][hapmap]
rs11070868	0.80[GIH][hapmap]
rs1133882	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11630084	0.82[JPT][hapmap];0.84[AFR][1000 genomes]
rs11630943	0.81[GIH][hapmap]
rs11632106	0.82[AFR][1000 genomes]
rs11636345	0.89[GIH][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.81[AFR][1000 genomes]
rs11637876	0.81[GIH][hapmap]
rs11638766	0.86[AFR][1000 genomes]
rs11638820	0.89[GIH][hapmap];0.98[LWK][hapmap];0.91[MKK][hapmap];0.86[AFR][1000 genomes]
rs12903707	0.89[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap]
rs12905283	0.81[GIH][hapmap];0.86[LWK][hapmap]
rs12908327	0.81[GIH][hapmap]
rs12917133	0.83[ASW][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.81[AFR][1000 genomes]
rs1350174	0.83[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1466276	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1545602	0.82[AFR][1000 genomes]
rs17526463	0.81[GIH][hapmap]
rs17526760	0.81[GIH][hapmap]
rs17611193	0.80[GIH][hapmap]
rs1811326	0.86[GIH][hapmap]
rs1840708	0.81[GIH][hapmap]
rs1902430	0.89[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1972689	0.89[GIH][hapmap]
rs2007355	0.82[GIH][hapmap]
rs2014638	0.91[GIH][hapmap]
rs2034856	0.82[GIH][hapmap];0.86[LWK][hapmap]
rs2034857	0.82[ASW][hapmap];0.81[GIH][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];0.81[AFR][1000 genomes]
rs2034858	0.82[ASW][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.81[AFR][1000 genomes]
rs2077743	0.83[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2168475	0.88[ASN][1000 genomes]
rs2252831	0.82[GIH][hapmap]
rs2303443	0.89[GIH][hapmap]
rs2414117	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2441780	0.80[GIH][hapmap]
rs2554327	0.82[GIH][hapmap]
rs2554336	0.89[GIH][hapmap]
rs2554349	0.83[CHB][hapmap];0.82[GIH][hapmap]
rs2570224	0.89[GIH][hapmap]
rs2570228	0.89[GIH][hapmap]
rs2570239	0.82[GIH][hapmap]
rs2570241	0.82[GIH][hapmap]
rs2570258	0.89[GIH][hapmap]
rs2593173	0.82[GIH][hapmap]
rs2623271	0.82[GIH][hapmap]
rs2912189	0.81[GIH][hapmap]
rs2916172	0.81[GIH][hapmap]
rs2916176	0.81[GIH][hapmap]
rs2929425	0.81[GIH][hapmap]
rs2959285	0.81[GIH][hapmap]
rs3751596	0.89[GIH][hapmap]
rs3794535	0.89[GIH][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap]
rs4238383	0.83[ASW][hapmap];0.89[GIH][hapmap];0.98[LWK][hapmap];0.91[MKK][hapmap];0.86[AFR][1000 genomes]
rs4502160	0.86[AFR][1000 genomes]
rs4622456	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4774602	0.89[GIH][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap]
rs4775978	0.81[AFR][1000 genomes]
rs4775983	0.89[GIH][hapmap]
rs526556	0.87[ASN][1000 genomes]
rs6493515	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6493518	0.84[AFR][1000 genomes]
rs6493519	0.81[AFR][1000 genomes]
rs6493520	0.81[GIH][hapmap]
rs6493523	0.89[GIH][hapmap]
rs6493525	0.81[GIH][hapmap]
rs6493526	0.82[GIH][hapmap]
rs689884	0.93[GIH][hapmap];0.88[MKK][hapmap]
rs7163176	0.90[ASN][1000 genomes]
rs7165585	0.83[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7166110	0.86[AFR][1000 genomes]
rs7173375	0.85[AFR][1000 genomes]
rs7174497	0.81[GIH][hapmap]
rs7174808	0.81[GIH][hapmap]
rs7181553	0.83[ASW][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];0.86[AFR][1000 genomes]
rs8024088	0.81[AFR][1000 genomes]
rs8024589	0.81[AFR][1000 genomes]
rs8028258	0.89[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs8028890	0.83[AFR][1000 genomes]
rs8028922	0.81[GIH][hapmap]
rs8035173	0.82[GIH][hapmap]

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	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:51984800-52018600	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:51991400-52018800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:51992200-52018800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:51999800-52018200	Weak transcription	Fetal Stomach	stomach
6	chr15:52000800-52024000	Weak transcription	Gastric	stomach
7	chr15:52001000-52018600	Weak transcription	Pancreas	Pancrea
8	chr15:52004800-52018600	Weak transcription	Spleen	Spleen
9	chr15:52006400-52018400	Weak transcription	Fetal Muscle Leg	muscle
10	chr15:52007000-52023400	Weak transcription	Brain Anterior Caudate	brain
11	chr15:52007800-52018200	Weak transcription	NHDF-Ad	bronchial
12	chr15:52008200-52023200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:52008400-52018400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:52008400-52023400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:52010800-52018400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:52010800-52018400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:52011200-52018400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:52011200-52018600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:52011400-52018800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:52011400-52023400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:52011600-52018400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:52011600-52023400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:52011800-52018200	Weak transcription	Hela-S3	cervix
24	chr15:52011800-52018200	Weak transcription	HMEC	breast
25	chr15:52012400-52024200	Weak transcription	Fetal Lung	lung
26	chr15:52012800-52018400	Weak transcription	Ovary	ovary
27	chr15:52013400-52018600	Weak transcription	Lung	lung
28	chr15:52013400-52018800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:52013400-52023600	Weak transcription	Colonic Mucosa	Colon
30	chr15:52013600-52018400	Weak transcription	Esophagus	oesophagus
31	chr15:52013600-52018400	Weak transcription	Left Ventricle	heart
32	chr15:52013600-52018800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:52013600-52019400	Weak transcription	Thymus	Thymus
34	chr15:52013600-52028200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:52013600-52028400	Weak transcription	Fetal Brain Female	brain
36	chr15:52013600-52028800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:52014000-52018200	Weak transcription	Brain Substantia Nigra	brain
38	chr15:52014000-52018200	Weak transcription	Osteobl	bone
39	chr15:52014000-52018400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:52014000-52018400	Weak transcription	NH-A	brain
41	chr15:52014000-52019200	Weak transcription	Aorta	Aorta
42	chr15:52014000-52023000	Weak transcription	Stomach Mucosa	stomach
43	chr15:52014200-52018000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:52014200-52018200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:52014400-52018400	Weak transcription	Psoas Muscle	Psoas
46	chr15:52014600-52018400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:52014600-52018400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:52014600-52018400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:52014600-52018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:52014600-52022600	Weak transcription	Fetal Thymus	thymus

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