Variant report

Variant	rs513680
Chromosome Location	chr15:41405662-41405663
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41404323..41407208-chr15:41574690..41577351,2	K562	blood:
2	chr15:41403941..41406164-chr15:41407398..41410541,4	MCF-7	breast:
3	chr15:41391555..41394241-chr15:41403159..41405692,2	K562	blood:

Variant related genes	Relation type
ENSG00000247556	Chromatin interaction
ENSG00000128908	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10152296	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070319	0.94[AMR][1000 genomes]
rs11070320	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11630905	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs16971263	0.83[AMR][1000 genomes]
rs16971463	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2007255	0.84[AMR][1000 genomes]
rs2412599	1.00[EUR][1000 genomes]
rs2412600	1.00[EUR][1000 genomes]
rs28455970	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28528813	0.89[AMR][1000 genomes]
rs2899010	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2925348	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2925349	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2927067	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2928147	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2928149	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2928150	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2928154	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2947492	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2947495	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2947496	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2955812	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3101435	0.83[AMR][1000 genomes]
rs3101438	1.00[AMR][1000 genomes]
rs3101441	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4468583	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs474351	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs480549	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs487779	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4923894	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4923895	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4924533	0.84[AMR][1000 genomes]
rs4924534	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs496499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs518137	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs525551	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs538903	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs56955512	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57008457	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs57385441	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58142514	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs59405359	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs690773	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs691069	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs691722	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs692703	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7162003	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7167166	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7172555	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173146	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7174223	1.00[EUR][1000 genomes]
rs7174513	1.00[AMR][1000 genomes]
rs7183191	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs73399092	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8032956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8034461	0.94[AMR][1000 genomes]
rs8035532	1.00[AMR][1000 genomes]
rs8043232	0.89[AMR][1000 genomes]
rs9806344	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv569230	chr15:41384649-41483682	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv904108	chr15:41384649-41486990	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41361200-41407200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:41383200-41406800	Weak transcription	A549	lung
3	chr15:41383800-41407400	Weak transcription	Esophagus	oesophagus
4	chr15:41384000-41407400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:41384400-41407400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:41385200-41406000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:41386200-41407400	Weak transcription	Aorta	Aorta
8	chr15:41386600-41407400	Weak transcription	Colonic Mucosa	Colon
9	chr15:41386800-41406800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:41386800-41406800	Weak transcription	Right Ventricle	heart
11	chr15:41386800-41407000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr15:41386800-41407200	Weak transcription	HSMMtube	muscle
13	chr15:41386800-41407400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:41387200-41406000	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:41387200-41406600	Weak transcription	Pancreas	Pancrea
16	chr15:41387400-41407200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:41388000-41406600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:41388200-41406600	Weak transcription	Adipose Nuclei	Adipose
19	chr15:41388400-41406400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:41388600-41405800	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:41388600-41406600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:41388600-41406600	Weak transcription	Ovary	ovary
23	chr15:41388600-41406600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:41388600-41406800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:41388600-41406800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:41388600-41406800	Weak transcription	Fetal Brain Female	brain
27	chr15:41388600-41406800	Weak transcription	Fetal Lung	lung
28	chr15:41388600-41407000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:41388600-41407000	Weak transcription	Fetal Kidney	kidney
30	chr15:41388600-41407200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr15:41388600-41407200	Weak transcription	Brain Anterior Caudate	brain
32	chr15:41388600-41407400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr15:41388800-41406200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:41388800-41406800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr15:41388800-41407000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:41388800-41407000	Weak transcription	Fetal Intestine Large	intestine
37	chr15:41389000-41405800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr15:41389000-41406600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:41389000-41406800	Weak transcription	HMEC	breast
40	chr15:41389200-41406800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:41389800-41406800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:41391000-41407400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:41391200-41406000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:41391600-41407000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:41392000-41406400	Weak transcription	Liver	Liver
46	chr15:41392000-41406800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr15:41395600-41406600	Weak transcription	Brain Substantia Nigra	brain
48	chr15:41395600-41407200	Weak transcription	HSMM	muscle
49	chr15:41396000-41407000	Weak transcription	NHDF-Ad	bronchial
50	chr15:41397400-41406600	Weak transcription	HUVEC	blood vessel

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