Variant report

Variant	rs11730728
Chromosome Location	chr4:119696679-119696680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119694892..119697227-chr4:120132083..120133760,2	K562	blood:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction
ENSG00000178636	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11724866	0.86[EUR][1000 genomes]
rs11735989	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945703	0.91[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12640223	0.86[EUR][1000 genomes]
rs12646268	0.84[EUR][1000 genomes]
rs12646298	0.85[EUR][1000 genomes]
rs12648682	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs12648778	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs13105145	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13105732	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13111664	0.86[EUR][1000 genomes]
rs13115157	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs13124091	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs13146440	0.95[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs13146816	0.95[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs13150663	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17324912	0.81[CHB][hapmap]
rs2029399	0.91[CEU][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2046779	0.95[CEU][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs2288307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087958	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs34091082	0.88[EUR][1000 genomes]
rs34270389	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34508500	0.88[EUR][1000 genomes]
rs34628947	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35023705	0.86[EUR][1000 genomes]
rs35071348	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35392662	0.89[EUR][1000 genomes]
rs35404779	0.89[EUR][1000 genomes]
rs35522890	0.86[EUR][1000 genomes]
rs35613641	0.86[EUR][1000 genomes]
rs35952841	0.86[EUR][1000 genomes]
rs36023173	0.86[EUR][1000 genomes]
rs3733517	0.91[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs66500248	0.86[EUR][1000 genomes]
rs66942289	0.86[EUR][1000 genomes]
rs67151421	0.87[EUR][1000 genomes]
rs67989872	0.88[EUR][1000 genomes]
rs6813357	0.91[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs6814447	0.86[EUR][1000 genomes]
rs6817440	0.81[CHB][hapmap]
rs6817790	0.86[EUR][1000 genomes]
rs6818241	0.86[EUR][1000 genomes]
rs6821350	0.88[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs6827740	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6829010	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6831197	0.86[EUR][1000 genomes]
rs6836005	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs6837652	0.86[EUR][1000 genomes]
rs6847706	0.95[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs6849714	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6852706	0.85[EUR][1000 genomes]
rs6853722	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855919	0.86[EUR][1000 genomes]
rs6857285	0.95[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs71610228	0.86[EUR][1000 genomes]
rs72679023	0.89[EUR][1000 genomes]
rs7653962	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs7662650	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7670182	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7681835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692721	0.91[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs7695602	0.95[CEU][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs7696543	0.89[EUR][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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11730728	C4orf31	cis	cerebellum	SCAN
rs11730728	FGF2	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
2	chr4:119678600-119717400	Weak transcription	Esophagus	oesophagus
3	chr4:119679000-119717600	Weak transcription	Colonic Mucosa	Colon
4	chr4:119684400-119704000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:119686800-119704600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:119687600-119711800	Weak transcription	Stomach Mucosa	stomach
7	chr4:119688400-119702400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:119688600-119696800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:119688600-119703600	Weak transcription	Lung	lung
10	chr4:119688600-119703800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:119688600-119705000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:119688600-119710000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:119688600-119712800	Weak transcription	Gastric	stomach
14	chr4:119688600-119715800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:119688600-119717400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:119688600-119717400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:119688600-119732600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:119688800-119703600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:119688800-119704000	Weak transcription	Primary B cells from cord blood	blood
20	chr4:119688800-119716800	Weak transcription	Fetal Kidney	kidney
21	chr4:119689000-119703600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:119689000-119703800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:119689200-119697600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:119689400-119709000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:119689400-119716200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:119689400-119716600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:119689400-119716800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr4:119689600-119703000	Weak transcription	Fetal Intestine Large	intestine
29	chr4:119689600-119703400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:119689600-119709400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:119689600-119717600	Weak transcription	K562	blood
32	chr4:119689800-119703400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:119689800-119708800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:119690000-119704000	Weak transcription	Dnd41	blood
35	chr4:119690000-119717600	Weak transcription	Primary T cells from cord blood	blood
36	chr4:119691600-119703200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:119691600-119703400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr4:119691600-119703800	Weak transcription	Placenta	Placenta
39	chr4:119691600-119703800	Weak transcription	GM12878-XiMat	blood
40	chr4:119692200-119703400	Weak transcription	HepG2	liver
41	chr4:119692400-119696800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:119692400-119698000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:119692600-119697600	Enhancers	NHEK	skin
44	chr4:119692600-119703400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr4:119693400-119698000	Enhancers	NHDF-Ad	bronchial
46	chr4:119693600-119697000	Enhancers	HSMMtube	muscle
47	chr4:119694000-119697400	Weak transcription	Fetal Thymus	thymus
48	chr4:119694000-119698200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:119694000-119698200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:119694000-119703000	Weak transcription	Duodenum Mucosa	Duodenum

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