Variant report

Variant	rs28624186
Chromosome Location	chr2:110352589-110352590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:110350487..110353137-chr2:110370144..110372434,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198142	Chromatin interaction
ENSG00000186522	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10496433	0.85[EUR][1000 genomes]
rs1560884	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1836211	0.80[EUR][1000 genomes]
rs2014730	0.80[EUR][1000 genomes]
rs2018352	0.82[ASN][1000 genomes]
rs2043462	0.82[ASN][1000 genomes]
rs28369323	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28513618	0.80[EUR][1000 genomes]
rs28588372	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28613553	0.80[EUR][1000 genomes]
rs2867277	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28800201	0.85[EUR][1000 genomes]
rs4953843	0.81[ASN][1000 genomes]
rs58012425	0.91[ASN][1000 genomes]
rs60272411	0.81[EUR][1000 genomes]
rs61049649	0.80[EUR][1000 genomes]
rs61215808	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61428642	0.80[EUR][1000 genomes]
rs61548546	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594041	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6705503	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6713646	0.85[EUR][1000 genomes]
rs6716287	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6723295	0.82[ASN][1000 genomes]
rs6760478	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72938271	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72940218	0.80[EUR][1000 genomes]
rs747445	0.81[ASN][1000 genomes]
rs7568492	0.85[EUR][1000 genomes]
rs7568799	0.81[EUR][1000 genomes]
rs7572991	0.85[EUR][1000 genomes]
rs7579996	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7590230	0.82[EUR][1000 genomes]
rs767628	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs892460	0.82[ASN][1000 genomes]
rs892464	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs919941	0.80[ASN][1000 genomes]
rs9330316	0.85[ASN][1000 genomes]
rs9751601	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28624186	ANKRD57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
4	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:110319200-110367400	Weak transcription	HSMMtube	muscle
7	chr2:110319400-110358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:110320600-110354600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:110324000-110370400	Weak transcription	Esophagus	oesophagus
10	chr2:110324600-110362200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:110329000-110369000	Weak transcription	Ovary	ovary
12	chr2:110329200-110359400	Weak transcription	NHLF	lung
13	chr2:110329200-110369400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:110329400-110359600	Weak transcription	NHDF-Ad	bronchial
15	chr2:110332200-110352600	Weak transcription	Fetal Lung	lung
16	chr2:110338600-110354600	Weak transcription	Right Atrium	heart
17	chr2:110338600-110357600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:110338800-110352600	Weak transcription	Fetal Intestine Large	intestine
19	chr2:110341600-110359400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:110341800-110359000	Weak transcription	Fetal Kidney	kidney
21	chr2:110343400-110357600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:110343400-110357600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:110343400-110358000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:110343400-110358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:110343400-110358600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:110343400-110358800	Weak transcription	Adipose Nuclei	Adipose
27	chr2:110343400-110362200	Weak transcription	Psoas Muscle	Psoas
28	chr2:110343400-110362200	Weak transcription	Osteobl	bone
29	chr2:110343600-110364400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:110344000-110357600	Weak transcription	Left Ventricle	heart
31	chr2:110344000-110358600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:110344400-110355000	Weak transcription	Aorta	Aorta
33	chr2:110344400-110358200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:110344400-110365800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:110344600-110362200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:110348600-110354000	Strong transcription	HepG2	liver
37	chr2:110348600-110357600	Weak transcription	Right Ventricle	heart
38	chr2:110348600-110359400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:110349200-110354600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:110349200-110355000	Weak transcription	Brain Angular Gyrus	brain
41	chr2:110349400-110362200	Weak transcription	Lung	lung
42	chr2:110349400-110364600	Weak transcription	HSMM	muscle
43	chr2:110349800-110354600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:110349800-110358600	Weak transcription	HUVEC	blood vessel
45	chr2:110349800-110359400	Weak transcription	Hela-S3	cervix
46	chr2:110349800-110362200	Weak transcription	A549	lung
47	chr2:110350200-110353400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:110350200-110365800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:110350200-110367000	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:110350400-110362200	Weak transcription	Fetal Intestine Small	intestine

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