Variant report

Variant	rs11897553
Chromosome Location	chr2:114512478-114512479
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:114512297..114513973-chr2:114517803..114519961,2	MCF-7	breast:
2	chr2:114510034..114517579-chr2:114643441..114655407,23	MCF-7	breast:
3	chr2:114511479..114519908-chr2:114641728..114650266,13	MCF-7	breast:
4	chr2:114511724..114513896-chr2:114718190..114720983,2	K562	blood:

Variant related genes	Relation type
ENSG00000115091	Chromatin interaction
ENSG00000270019	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10168234	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10199704	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10200355	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10205467	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206174	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10938	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11679707	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11682259	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695798	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11901060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711784	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12711786	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13006627	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13029093	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13034531	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13397540	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13405475	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13416930	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1349157	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1584434	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17048473	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2122095	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305254	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2418915	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35432356	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35667749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4849264	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4849265	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4849266	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4849269	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56213422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56376185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58473055	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542171	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6704673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731402	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6739072	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6741521	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67850681	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561176	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7578249	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586800	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7587218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7590375	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7592689	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600550	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs935644	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9798411	0.84[AMR][1000 genomes];0.84[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	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv2883	chr2:114507889-114535199	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	esv3443848	chr2:114512467-114512812	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11897553	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs11897553	RPL23AP7	cis	Muscle Skeletal	GTEx
rs11897553	PS1TP4	Cis_1M	lymphoblastoid	RTeQTL
rs11897553	SLC35F5	cis	Skin Sun Exposed Lower leg	GTEx
rs11897553	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs11897553	RPL23AP7	cis	Whole Blood	GTEx
rs11897553	DDX11L2	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:114461400-114513200	Weak transcription	Small Intestine	intestine
3	chr2:114468800-114512800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:114481200-114513000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:114484600-114512600	Weak transcription	Aorta	Aorta
6	chr2:114487200-114513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:114488400-114512600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:114492200-114513000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:114499200-114512600	Weak transcription	Esophagus	oesophagus
10	chr2:114500600-114512600	Weak transcription	Hela-S3	cervix
11	chr2:114502200-114513000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:114504000-114512600	Weak transcription	Brain Substantia Nigra	brain
13	chr2:114504600-114512600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:114505000-114513000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:114505000-114513200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:114506800-114512800	Weak transcription	Colonic Mucosa	Colon
17	chr2:114507000-114512600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:114507000-114512600	Weak transcription	Right Ventricle	heart
19	chr2:114507000-114512800	Weak transcription	Fetal Thymus	thymus
20	chr2:114507000-114513000	Weak transcription	Gastric	stomach
21	chr2:114507000-114513000	Weak transcription	Pancreas	Pancrea
22	chr2:114507000-114513400	Weak transcription	Spleen	Spleen
23	chr2:114507400-114512600	Weak transcription	Psoas Muscle	Psoas
24	chr2:114508600-114512600	Weak transcription	Thymus	Thymus
25	chr2:114508800-114512600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:114508800-114513000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:114508800-114513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:114508800-114513400	Weak transcription	Lung	lung
29	chr2:114509000-114512600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:114509000-114512600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:114509000-114512600	Weak transcription	Ovary	ovary
32	chr2:114509000-114513000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:114509200-114512600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:114509200-114513000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:114509400-114512800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:114509400-114513400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:114509400-114513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:114509600-114512600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:114509600-114512600	Weak transcription	Left Ventricle	heart
40	chr2:114510400-114513000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr2:114510600-114512800	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:114510600-114513000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:114510600-114513000	Weak transcription	Placenta	Placenta
44	chr2:114511200-114512600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:114511200-114515000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:114511600-114512600	Enhancers	Brain Angular Gyrus	brain
47	chr2:114511600-114512600	Weak transcription	Fetal Stomach	stomach
48	chr2:114511600-114515200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:114511800-114512600	Enhancers	Liver	Liver
50	chr2:114511800-114512600	Enhancers	Fetal Lung	lung

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