Variant report

Variant	rs3811609
Chromosome Location	chr2:191354491-191354492
allele	C/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	NANOG	chr2:191354303-191354506	H1-hESC	embryonic stem cell:	n/a	n/a
2	STAT3	chr2:191354419-191354619	MCF10A-Er-Src	breast:	n/a	chr2:191354598-191354605 chr2:191354451-191354465

Variant related genes	Relation type
MFSD6	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10193212	0.83[YRI][hapmap]
rs11897266	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464923	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12472240	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12473460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12613365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613807	0.83[YRI][hapmap]
rs12615925	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12619125	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12619560	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621493	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12622496	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12693576	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12987797	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13013848	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13019278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13028201	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13029743	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13391723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34274882	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34417560	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34825614	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36055519	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4073873	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4129081	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4264585	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4324342	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4586658	0.89[LWK][hapmap]
rs4853508	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4853709	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4853718	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4853720	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55754136	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55987230	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6434400	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6707773	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707846	0.84[ASN][1000 genomes]
rs6711006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72911109	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560318	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7584794	0.85[LWK][hapmap]
rs7601745	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7608180	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3811609	INPP1	cis	parietal	SCAN
rs3811609	HIBCH	cis	parietal	SCAN
rs3811609	HIBCH	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191332800-191356200	Weak transcription	Aorta	Aorta
2	chr2:191332800-191364200	Weak transcription	Spleen	Spleen
3	chr2:191333400-191355400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:191334200-191370200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:191334400-191355400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:191334800-191394800	Weak transcription	HSMMtube	muscle
7	chr2:191335400-191366200	Weak transcription	Hela-S3	cervix
8	chr2:191342800-191356000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:191343000-191372000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:191343200-191356000	Weak transcription	Fetal Kidney	kidney
11	chr2:191343400-191373800	Weak transcription	Colonic Mucosa	Colon
12	chr2:191343600-191356000	Weak transcription	K562	blood
13	chr2:191346800-191364200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:191346800-191364800	Weak transcription	Gastric	stomach
15	chr2:191347000-191364600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:191347400-191364200	Weak transcription	Stomach Mucosa	stomach
17	chr2:191348400-191356000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:191349000-191362200	Weak transcription	A549	lung
19	chr2:191349000-191366200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:191349600-191394600	Weak transcription	NHLF	lung
21	chr2:191351200-191355400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:191351200-191355400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:191351200-191356000	Weak transcription	Brain Germinal Matrix	brain
24	chr2:191351200-191362000	Weak transcription	Brain Angular Gyrus	brain
25	chr2:191351200-191364200	Weak transcription	Right Ventricle	heart
26	chr2:191351200-191364800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:191351200-191369600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:191351200-191373400	Weak transcription	Small Intestine	intestine
29	chr2:191351400-191354600	Weak transcription	Brain Anterior Caudate	brain
30	chr2:191351400-191356000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:191351400-191356000	Weak transcription	Pancreas	Pancrea
32	chr2:191351400-191362000	Weak transcription	Brain Substantia Nigra	brain
33	chr2:191351400-191385400	Weak transcription	NHEK	skin
34	chr2:191351800-191356000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:191351800-191356000	Weak transcription	Adipose Nuclei	Adipose
36	chr2:191352000-191356600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:191352000-191364400	Weak transcription	Placenta	Placenta
38	chr2:191352200-191380600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:191352400-191356000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr2:191352400-191381600	Weak transcription	Osteobl	bone
41	chr2:191352600-191356400	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:191352800-191356000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:191353000-191354600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
44	chr2:191353000-191354800	Genic enhancers	Primary T cells from cord blood	blood
45	chr2:191353000-191355600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:191353000-191356000	Strong transcription	Primary B cells from cord blood	blood
47	chr2:191353000-191356000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:191353000-191356000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:191353000-191356600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr2:191353000-191356600	Strong transcription	Rectal Mucosa Donor 31	rectum

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