Variant report

Variant	rs6713112
Chromosome Location	chr2:30886362-30886363
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:30883787..30887664-chr2:30907085..30909413,4	K562	blood:
2	chr2:30410152..30414990-chr2:30883111..30886587,5	K562	blood:
3	chr2:30867045..30872289-chr2:30881194..30886841,8	K562	blood:
4	chr2:30444710..30446228-chr2:30884155..30887092,2	K562	blood:
5	chr2:30730220..30735508-chr2:30883142..30886584,5	K562	blood:
6	chr2:30884077..30887138-chr2:30917799..30920248,4	K562	blood:
7	chr2:30883151..30886759-chr2:30927667..30934469,9	K562	blood:
8	chr2:30884451..30886739-chr2:30899746..30902307,4	K562	blood:
9	chr2:30885114..30887273-chr2:30896236..30898682,2	K562	blood:
10	chr2:30882862..30887095-chr2:30947474..30950247,3	K562	blood:
11	chr2:30883186..30886745-chr2:30927667..30931555,5	K562	blood:
12	chr2:30885089..30887091-chr2:30887227..30889591,3	MCF-7	breast:
13	chr2:30880506..30884511-chr2:30884775..30887902,3	MCF-7	breast:
14	chr2:30387277..30390293-chr2:30882898..30886661,5	K562	blood:
15	chr2:30809203..30812832-chr2:30884056..30887264,3	K562	blood:
16	chr2:30884077..30886953-chr2:30917137..30920248,5	K562	blood:
17	chr2:30883581..30886486-chr2:30904225..30906593,3	K562	blood:
18	chr2:30388130..30392158-chr2:30882898..30886661,6	K562	blood:
19	chr2:30884154..30887664-chr2:30907085..30910556,4	K562	blood:
20	chr2:29100191..29103125-chr2:30883778..30886607,2	K562	blood:
21	chr2:30670026..30672853-chr2:30882772..30886390,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172954	Chromatin interaction
ENSG00000207187	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10180872	1.00[JPT][hapmap]
rs10203381	1.00[JPT][hapmap]
rs10207070	1.00[JPT][hapmap]
rs10207451	0.83[ASN][1000 genomes]
rs1026066	1.00[JPT][hapmap]
rs1031236	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11127283	1.00[ASN][1000 genomes]
rs12994945	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12997116	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013282	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429099	1.00[JPT][hapmap]
rs13430761	1.00[JPT][hapmap]
rs1869427	1.00[ASN][1000 genomes]
rs1901910	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028961	0.82[AMR][1000 genomes]
rs2363078	1.00[ASN][1000 genomes]
rs34585086	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34658981	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35148876	0.83[ASN][1000 genomes]
rs4372952	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62142162	1.00[ASN][1000 genomes]
rs62142164	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743856	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71444466	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6713112	FAM179A	cis	cerebellum	SCAN
rs6713112	LCLAT1	cis	cerebellum	SCAN
rs6713112	SLC4A1AP	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30882800-30889600	Enhancers	Fetal Muscle Leg	muscle
2	chr2:30883600-30887400	Enhancers	HSMMtube	muscle
3	chr2:30883600-30890400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:30884000-30889000	Weak transcription	Psoas Muscle	Psoas
5	chr2:30884400-30886600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:30884400-30890000	Enhancers	NHDF-Ad	bronchial
7	chr2:30884600-30888000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:30884600-30888200	Enhancers	Fetal Muscle Trunk	muscle
9	chr2:30884600-30889400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:30884600-30889600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr2:30884800-30886400	Enhancers	Stomach Smooth Muscle	stomach
12	chr2:30884800-30886600	Enhancers	Fetal Stomach	stomach
13	chr2:30884800-30887200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:30884800-30889200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:30885200-30886400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:30885200-30886400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:30885200-30887200	Enhancers	NHLF	lung
18	chr2:30885200-30887400	Enhancers	NH-A	brain
19	chr2:30885200-30889400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:30885400-30886400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:30885400-30886400	Enhancers	HSMM	muscle
22	chr2:30885400-30889000	Enhancers	NHEK	skin
23	chr2:30885800-30887400	Enhancers	A549	lung
24	chr2:30886000-30886400	Enhancers	Fetal Intestine Small	intestine
25	chr2:30886000-30887000	Weak transcription	Osteobl	bone
26	chr2:30886000-30887200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:30886000-30888800	Weak transcription	Left Ventricle	heart
28	chr2:30886000-30888800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:30886200-30886800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:30886200-30887200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:30886200-30887200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:30886200-30889600	Enhancers	HMEC	breast

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