Variant report

Variant	rs4853713
Chromosome Location	chr2:191330861-191330862
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:191330813-191331147	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191324546..191326612-chr2:191328587..191331332,2	K562	blood:

Variant related genes	Relation type
MFSD6	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10182754	0.84[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190082	0.94[CHB][hapmap]
rs10193212	0.84[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931452	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10931458	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs1128723	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12052514	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12053190	0.89[CHB][hapmap]
rs12472081	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12475614	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12613807	0.84[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12693574	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693575	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12998288	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13020324	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13409841	0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2354878	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35095338	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811607	0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4258824	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs4340549	0.89[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs4439990	0.89[CHB][hapmap]
rs4641969	0.89[CHB][hapmap]
rs4853507	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4853702	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4853705	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4853710	0.92[YRI][hapmap]
rs4853711	0.85[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434391	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6707691	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6731287	0.89[CHB][hapmap]
rs7557681	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7564829	0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7596573	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7603607	0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9646748	0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9646815	0.86[EUR][1000 genomes];0.93[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	esv33134	chr2:191318791-191365710	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4853713	FLJ20160	cis	multi-tissue	Pritchard
rs4853713	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL
rs4853713	TMEM194B	cis	Adipose Subcutaneous	GTEx
rs4853713	MFSD6	cis	Artery Tibial	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191302400-191331000	Weak transcription	A549	lung
2	chr2:191303800-191331600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:191303800-191332600	Weak transcription	Fetal Intestine Large	intestine
4	chr2:191306600-191351000	Weak transcription	Pancreas	Pancrea
5	chr2:191309400-191331400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:191310400-191331600	Weak transcription	Stomach Mucosa	stomach
7	chr2:191311600-191331400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:191311800-191331400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:191311800-191331400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:191311800-191331600	Weak transcription	Ovary	ovary
11	chr2:191312000-191332400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:191313000-191331400	Weak transcription	HSMMtube	muscle
13	chr2:191313000-191333600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:191314000-191331600	Weak transcription	Fetal Kidney	kidney
15	chr2:191316600-191331200	Weak transcription	NHLF	lung
16	chr2:191317600-191331600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:191319400-191331800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:191319400-191332000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:191322000-191331600	Weak transcription	Fetal Brain Female	brain
20	chr2:191322000-191335800	Weak transcription	Esophagus	oesophagus
21	chr2:191322200-191331400	Weak transcription	Fetal Stomach	stomach
22	chr2:191322600-191335600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:191322800-191331200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr2:191323000-191331000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:191323000-191334600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:191323200-191332400	Weak transcription	Fetal Intestine Small	intestine
27	chr2:191323200-191335800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:191323400-191333600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr2:191324000-191331400	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:191324600-191332400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:191324800-191331200	Weak transcription	Fetal Lung	lung
32	chr2:191325400-191331400	Weak transcription	Fetal Heart	heart
33	chr2:191325400-191332600	Weak transcription	Gastric	stomach
34	chr2:191325600-191331600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:191325600-191335800	Weak transcription	Lung	lung
36	chr2:191325600-191346200	Weak transcription	Right Ventricle	heart
37	chr2:191327200-191331000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:191327600-191353000	Weak transcription	Primary B cells from cord blood	blood
39	chr2:191327800-191331400	Weak transcription	Brain Angular Gyrus	brain
40	chr2:191327800-191331400	Weak transcription	Right Atrium	heart
41	chr2:191327800-191332200	Weak transcription	Aorta	Aorta
42	chr2:191327800-191332200	Weak transcription	Spleen	Spleen
43	chr2:191328000-191331000	Weak transcription	Brain Substantia Nigra	brain
44	chr2:191328000-191331600	Weak transcription	Brain Anterior Caudate	brain
45	chr2:191328200-191331400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:191328800-191332800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:191328800-191334400	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr2:191328800-191334600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr2:191329000-191331600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:191329400-191331200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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