Variant report

Variant	rs11724023
Chromosome Location	chr4:95558854-95558855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95557063..95559920-chr4:95560261..95562181,2	K562	blood:
2	chr4:95540920..95543603-chr4:95558219..95560946,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10031423	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10033326	0.88[CEU][hapmap]
rs1043853	0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs1048627	0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs1056773	0.84[EUR][1000 genomes]
rs11097433	0.86[EUR][1000 genomes]
rs11097434	0.83[EUR][1000 genomes]
rs11097435	0.84[EUR][1000 genomes]
rs11723532	0.91[EUR][1000 genomes]
rs11725850	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11732668	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs11732687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734014	0.92[EUR][1000 genomes]
rs12331240	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs12331253	0.85[EUR][1000 genomes]
rs12500426	0.85[CEU][hapmap]
rs12507763	0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12511111	0.86[EUR][1000 genomes]
rs12639623	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs12639887	0.92[CEU][hapmap];0.87[MEX][hapmap];0.83[EUR][1000 genomes]
rs12639980	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12641023	0.93[EUR][1000 genomes]
rs12642449	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs12643849	0.85[EUR][1000 genomes]
rs12643867	0.85[EUR][1000 genomes]
rs12649976	0.96[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12650641	0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs13110828	0.87[EUR][1000 genomes]
rs13122786	0.89[CEU][hapmap]
rs13130496	0.87[EUR][1000 genomes]
rs13135257	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs14082	0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs1472961	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1472962	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1543013	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs2047025	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2280002	0.87[EUR][1000 genomes]
rs2452601	0.88[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs28740868	0.81[EUR][1000 genomes]
rs2902987	0.85[EUR][1000 genomes]
rs34403066	0.92[EUR][1000 genomes]
rs34438564	0.93[EUR][1000 genomes]
rs34507709	0.87[EUR][1000 genomes]
rs35959898	0.89[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs3805263	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs3805264	0.86[EUR][1000 genomes]
rs3805266	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs3943	0.84[EUR][1000 genomes]
rs4634230	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs4699567	0.93[EUR][1000 genomes]
rs5013417	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs56921499	0.84[EUR][1000 genomes]
rs60195134	0.92[EUR][1000 genomes]
rs6532495	0.86[EUR][1000 genomes]
rs6532496	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs6532497	0.86[EUR][1000 genomes]
rs6829381	0.89[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs6854173	0.88[CEU][hapmap]
rs71601224	0.92[EUR][1000 genomes]
rs7662466	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs7690296	0.89[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs7697149	0.81[EUR][1000 genomes]
rs902981	0.85[CEU][hapmap]
rs951613	0.89[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs973995	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11724023	FAM190A	cis	cerebellum	SCAN
rs11724023	PDLIM5	cis	parietal	SCAN
rs11724023	ATOH1	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
2	chr4:95497200-95569400	Weak transcription	Esophagus	oesophagus
3	chr4:95515000-95562000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:95525000-95569600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:95525000-95586400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:95525000-95590000	Weak transcription	Lung	lung
7	chr4:95525400-95562200	Weak transcription	NHLF	lung
8	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
9	chr4:95533800-95594200	Weak transcription	Gastric	stomach
10	chr4:95537000-95563000	Weak transcription	K562	blood
11	chr4:95537600-95573400	Weak transcription	Spleen	Spleen
12	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
13	chr4:95538000-95585200	Weak transcription	Colonic Mucosa	Colon
14	chr4:95538200-95582600	Weak transcription	Hela-S3	cervix
15	chr4:95538200-95586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:95538600-95587000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:95539800-95561000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:95540000-95560600	Weak transcription	HepG2	liver
19	chr4:95540000-95566800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:95540000-95587000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:95540400-95561400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:95540400-95570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:95541000-95572600	Weak transcription	Small Intestine	intestine
25	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
26	chr4:95541400-95559200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:95541400-95560800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr4:95541400-95561200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr4:95541400-95580200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:95541600-95561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:95541600-95571400	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:95543000-95586000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:95543000-95586400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:95545000-95561400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:95545200-95559400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:95545600-95560600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr4:95546000-95560400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:95546600-95560400	Weak transcription	Adipose Nuclei	Adipose
39	chr4:95547800-95573000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:95549000-95586600	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:95551200-95563600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:95551400-95560400	Weak transcription	Liver	Liver
43	chr4:95553000-95560000	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:95553000-95560200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:95554800-95559000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:95555200-95566600	Weak transcription	Fetal Intestine Large	intestine
47	chr4:95555200-95578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:95555200-95581800	Weak transcription	Ovary	ovary
49	chr4:95555400-95559400	Weak transcription	HMEC	breast
50	chr4:95555400-95560000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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