Variant report

Variant	rs13005834
Chromosome Location	chr2:190008192-190008193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:190007614..190008526-chr2:190276902..190277807,3	K562	blood:
2	chr2:190007586..190008586-chr2:190152561..190153255,4	K562	blood:
3	chr2:190007524..190008539-chr2:190152002..190153324,12	MCF-7	breast:
4	chr2:190007040..190008928-chr2:190150245..190153733,35	MCF-7	breast:
5	chr2:190007645..190008347-chr2:190272146..190272703,2	MCF-7	breast:
6	chr2:44905140..44905661-chr2:190008031..190008552,2	MCF-7	breast:
7	chr2:190006464..190008527-chr2:190011142..190013874,2	MCF-7	breast:
8	chr2:190007645..190008457-chr21:9825917..9826742,2	MCF-7	breast:
9	chr2:190007947..190008562-chr2:190212282..190212800,2	K562	blood:
10	chr2:189959189..189959717-chr2:190007634..190008313,2	K562	blood:
11	chr14:47401862..47402382-chr2:190007804..190008571,2	MCF-7	breast:
12	chr2:190007607..190008525-chr2:190276403..190277763,5	MCF-7	breast:
13	chr2:190007941..190008744-chr2:190146380..190147371,2	MCF-7	breast:
14	chr2:190007573..190008510-chr2:190089119..190090066,2	MCF-7	breast:
15	chr2:190007864..190009528-chr2:190088531..190091177,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000264063	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10165127	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10165257	0.92[EUR][1000 genomes]
rs1016622	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10931401	0.92[EUR][1000 genomes]
rs10931411	0.82[EUR][1000 genomes]
rs11901914	0.95[EUR][1000 genomes]
rs12618316	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12999125	0.84[AFR][1000 genomes]
rs13005714	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13006065	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13013089	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13019651	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13020999	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13024858	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13028226	0.80[AFR][1000 genomes]
rs13030984	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356166	0.82[AFR][1000 genomes]
rs1399991	0.80[AFR][1000 genomes]
rs1464135	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1515864	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1515869	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1533618	0.88[EUR][1000 genomes]
rs1546617	0.84[AFR][1000 genomes]
rs1949327	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1983318	0.81[AFR][1000 genomes]
rs2138373	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36019389	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4417749	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667263	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667266	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667268	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4667271	0.88[EUR][1000 genomes]
rs4667275	0.82[EUR][1000 genomes]
rs62182417	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6434324	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6434325	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6728877	0.82[AFR][1000 genomes]
rs6737071	0.82[AFR][1000 genomes]
rs6741804	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749559	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6752781	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7560973	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7593860	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7599222	0.88[EUR][1000 genomes]
rs7606337	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9288163	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13005834	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189968600-190012000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:189981400-190014800	Weak transcription	Fetal Stomach	stomach
3	chr2:189984000-190016800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:189986000-190008800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:189993800-190017000	Weak transcription	Ovary	ovary
6	chr2:189994200-190010600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:189995400-190009000	Weak transcription	Adipose Nuclei	Adipose
8	chr2:189996000-190008800	Weak transcription	NHLF	lung
9	chr2:189997000-190008600	Weak transcription	NH-A	brain
10	chr2:189999000-190009400	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:190000400-190013600	Weak transcription	Left Ventricle	heart
12	chr2:190002400-190008400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:190002600-190009000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:190002800-190008800	Weak transcription	Osteobl	bone
15	chr2:190003000-190008800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:190003600-190014600	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:190006600-190008400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:190006600-190011800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:190007200-190008200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:190007400-190008200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:190007400-190008600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:190007400-190008800	Enhancers	A549	lung
23	chr2:190007400-190009200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:190007800-190008400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr2:190007800-190008400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr2:190007800-190008400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:190007800-190008400	Enhancers	Liver	Liver
28	chr2:190007800-190008400	Genic enhancers	NHDF-Ad	bronchial
29	chr2:190007800-190009600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:190007800-190010600	Strong transcription	HSMM	muscle
31	chr2:190008000-190008800	Weak transcription	Aorta	Aorta
32	chr2:190008000-190009000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:190008000-190009000	Enhancers	HSMMtube	muscle
34	chr2:190008000-190009200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:190008000-190010000	Enhancers	Fetal Lung	lung
36	chr2:190008000-190014800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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