Variant report

Variant	rs11964533
Chromosome Location	chr6:110059000-110059001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10499052	0.89[CEU][hapmap]
rs10499053	0.80[CEU][hapmap]
rs11968978	1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12208933	0.82[YRI][hapmap]
rs12526189	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12529505	0.89[CEU][hapmap]
rs12661287	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191444	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13194387	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13195462	0.80[EUR][1000 genomes]
rs13196280	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13197056	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13203636	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13204787	0.89[CEU][hapmap]
rs13207864	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13211604	0.94[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13212535	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1321328	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv5436	chr6:110052812-110097662	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11964533	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs11964533	SMPD2	cis	Whole Blood	GTEx
rs11964533	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs11964533	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
2	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:110034400-110060800	Weak transcription	Fetal Stomach	stomach
5	chr6:110034800-110059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
8	chr6:110035200-110065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
11	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
12	chr6:110035800-110065000	Weak transcription	HSMM	muscle
13	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
14	chr6:110039000-110081000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:110039800-110062000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:110040800-110062000	Weak transcription	Thymus	Thymus
17	chr6:110041000-110064800	Weak transcription	Gastric	stomach
18	chr6:110041000-110065000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:110041000-110065000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:110041400-110081000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:110042200-110088800	Weak transcription	Fetal Intestine Small	intestine
22	chr6:110042400-110089000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
24	chr6:110045800-110064800	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:110047000-110067200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:110047200-110084000	Weak transcription	Small Intestine	intestine
27	chr6:110047600-110068800	Weak transcription	Dnd41	blood
28	chr6:110048600-110089800	Weak transcription	Fetal Kidney	kidney
29	chr6:110048800-110062000	Strong transcription	Primary B cells from cord blood	blood
30	chr6:110050400-110065800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:110050400-110078400	Weak transcription	Fetal Brain Male	brain
32	chr6:110053400-110060800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr6:110054200-110063200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:110055000-110064800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:110055400-110059600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:110055400-110065000	Weak transcription	Osteobl	bone
37	chr6:110055800-110059200	Strong transcription	Liver	Liver
38	chr6:110055800-110063000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr6:110056000-110059200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:110056000-110060000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr6:110056000-110060400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr6:110056000-110061600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr6:110056000-110066600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:110056400-110060200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:110056400-110062400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:110056400-110063400	Strong transcription	Primary T cells from cord blood	blood
47	chr6:110056600-110063000	Strong transcription	Primary hematopoietic stem cells	blood
48	chr6:110056800-110059200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr6:110056800-110059200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr6:110056800-110067400	Weak transcription	Fetal Lung	lung

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