Variant report

Variant	rs3757238
Chromosome Location	chr6:109758835-109758836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:109758027-109758842	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109747606..109757389-chr6:109757828..109761794,11	K562	blood:
2	chr6:109755900..109759113-chr6:109760239..109764541,6	MCF-7	breast:
3	chr6:109751127..109754853-chr6:109756908..109760360,4	K562	blood:
4	chr6:109756751..109759661-chr6:109767137..109769430,2	MCF-7	breast:
5	chr6:109747606..109750215-chr6:109758639..109760987,2	K562	blood:

No data

Variant related genes	Relation type
SMPD2	TF binding region
ENSG00000239160	TF binding region
ENSG00000239160	Chromatin interaction
ENSG00000135587	Chromatin interaction
ENSG00000185250	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11753645	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11757877	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12524502	0.89[EUR][1000 genomes]
rs12528566	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12528712	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13192476	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13195517	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13199519	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13203252	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1322818	0.81[AMR][1000 genomes]
rs2275652	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34131679	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34292461	0.81[AMR][1000 genomes]
rs34320275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34533653	0.81[AMR][1000 genomes]
rs35969918	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799835	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3799840	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4428538	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61076041	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61233650	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61318425	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67857472	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6929208	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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	nsv823818	chr6:109757222-109761294	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3757238	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs3757238	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs3757238	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs3757238	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs3757238	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109721200-109760600	Weak transcription	Fetal Brain Female	brain
2	chr6:109725800-109760800	Weak transcription	Brain Anterior Caudate	brain
3	chr6:109736600-109760800	Weak transcription	Brain Angular Gyrus	brain
4	chr6:109745600-109760800	Weak transcription	Gastric	stomach
5	chr6:109750800-109760200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:109750800-109760400	Weak transcription	Ovary	ovary
7	chr6:109750800-109760800	Weak transcription	Brain Substantia Nigra	brain
8	chr6:109751000-109760200	Weak transcription	Osteobl	bone
9	chr6:109751000-109760800	Weak transcription	Right Atrium	heart
10	chr6:109751200-109760400	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:109751200-109761400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:109751400-109760800	Weak transcription	Fetal Stomach	stomach
13	chr6:109751600-109760400	Weak transcription	NHEK	skin
14	chr6:109753800-109760800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:109754000-109760800	Weak transcription	Pancreas	Pancrea
16	chr6:109754800-109760400	Weak transcription	K562	blood
17	chr6:109754800-109760600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:109756000-109760800	Weak transcription	Spleen	Spleen
19	chr6:109756200-109760200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:109756200-109760400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:109756400-109760600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:109756800-109761400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:109757200-109760400	Weak transcription	Fetal Intestine Small	intestine
24	chr6:109757200-109760600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:109758400-109759200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:109758600-109760800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:109758600-109760800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr6:109758800-109760600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:109758800-109760600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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