Variant report

Variant	rs57640930
Chromosome Location	chr5:14405231-14405232
allele	C/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	chr5:14405212-14405825	PANC-1	pancreas:	n/a	n/a
2	RAD21	chr5:14405067-14405993	SK-N-SH	brain:	n/a	chr5:14405491-14405505
3	CTCF	chr5:14405199-14406264	SK-N-SH	brain:	n/a	chr5:14405582-14405598 chr5:14405576-14405597 chr5:14405581-14405599

No.	Distal block	Cell Line	Cell type
1	chr5:14399431..14402316-chr5:14403363..14405249,2	K562	blood:
2	chr5:14405228..14405866-chr5:14648409..14649049,2	MCF-7	breast:
3	chr5:13976900..13977474-chr5:14404551..14405480,2	MCF-7	breast:

Variant related genes	Relation type
TRIO	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10866506	0.89[EUR][1000 genomes]
rs10866507	0.89[EUR][1000 genomes]
rs11949756	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11950000	1.00[EUR][1000 genomes]
rs11959397	0.89[EUR][1000 genomes]
rs12109453	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12109756	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12109880	0.89[EUR][1000 genomes]
rs12110161	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12110267	0.89[EUR][1000 genomes]
rs16903421	0.89[EUR][1000 genomes]
rs16903423	0.89[EUR][1000 genomes]
rs16903428	0.89[EUR][1000 genomes]
rs16903434	0.89[EUR][1000 genomes]
rs16903453	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs16903460	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16903464	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16903497	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs16903509	0.89[EUR][1000 genomes]
rs28416767	0.89[EUR][1000 genomes]
rs28482202	0.89[EUR][1000 genomes]
rs28548493	0.89[EUR][1000 genomes]
rs35373258	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56689214	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57017859	0.89[EUR][1000 genomes]
rs58260094	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59371168	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs59405120	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs60123555	0.82[AMR][1000 genomes]
rs60534900	0.84[AMR][1000 genomes]
rs60738268	0.89[EUR][1000 genomes]
rs60871697	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs60892841	0.84[EUR][1000 genomes]
rs61059406	0.89[EUR][1000 genomes]
rs61469842	0.84[EUR][1000 genomes]
rs62344979	0.89[EUR][1000 genomes]
rs62344981	0.86[EUR][1000 genomes]
rs62344983	0.89[EUR][1000 genomes]
rs62345009	0.84[EUR][1000 genomes]
rs62345012	0.89[EUR][1000 genomes]
rs62345015	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62345048	0.89[EUR][1000 genomes]
rs66554336	0.89[EUR][1000 genomes]
rs6860137	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6860252	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6883134	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6894866	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs73061636	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7706484	0.89[EUR][1000 genomes]
rs7715916	0.88[AFR][1000 genomes];0.91[EUR][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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
2	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr5:14363800-14430600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:14387200-14405800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:14388800-14407200	Weak transcription	Small Intestine	intestine
6	chr5:14392200-14406600	Weak transcription	Primary T cells from cord blood	blood
7	chr5:14392400-14406000	Weak transcription	Fetal Heart	heart
8	chr5:14392400-14426800	Weak transcription	Psoas Muscle	Psoas
9	chr5:14393600-14413600	Strong transcription	Primary B cells from cord blood	blood
10	chr5:14395200-14406600	Weak transcription	Fetal Kidney	kidney
11	chr5:14395800-14406000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:14395800-14406000	Weak transcription	Brain Substantia Nigra	brain
13	chr5:14397400-14405400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:14397600-14405600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:14397600-14406200	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:14398200-14406000	Weak transcription	Thymus	Thymus
17	chr5:14398400-14406000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:14398600-14406000	Weak transcription	Esophagus	oesophagus
19	chr5:14398800-14406200	Weak transcription	Aorta	Aorta
20	chr5:14399000-14419800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:14399600-14416400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr5:14400200-14413400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr5:14400400-14405400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:14400400-14406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:14400600-14415000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:14400800-14408600	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:14400800-14416000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:14401000-14405400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:14401000-14406600	Weak transcription	Left Ventricle	heart
30	chr5:14401200-14405400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr5:14401200-14406200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:14401200-14407400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr5:14401400-14405800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:14401400-14406200	Weak transcription	Colon Smooth Muscle	Colon
35	chr5:14401400-14406600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:14401600-14406000	Weak transcription	Colonic Mucosa	Colon
37	chr5:14401600-14407400	Strong transcription	Fetal Muscle Leg	muscle
38	chr5:14401800-14405800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:14401800-14407200	Weak transcription	Fetal Brain Male	brain
40	chr5:14402000-14406000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:14402000-14406000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr5:14402200-14405400	Strong transcription	NHLF	lung
43	chr5:14402400-14405800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:14402600-14405400	Weak transcription	HMEC	breast
45	chr5:14402600-14406400	Weak transcription	Hela-S3	cervix
46	chr5:14402600-14407200	Strong transcription	Fetal Stomach	stomach
47	chr5:14402600-14407600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:14402800-14405400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:14402800-14405400	Weak transcription	Placenta	Placenta
50	chr5:14403000-14405800	Weak transcription	H1 Cell Line	embryonic stem cell

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