Variant report

Variant	rs11079750
Chromosome Location	chr17:45149515-45149516
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	POLR2A	chr17:45149346-45149639	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45148479..45151206-chr17:45175479..45177922,2	K562	blood:

Variant related genes	Relation type
ENSG00000262879	TF binding region
ENSG00000262879	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10514915	0.89[ASN][1000 genomes]
rs1052586	0.81[CEU][hapmap]
rs11079745	0.84[CEU][hapmap]
rs11079748	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079752	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11649887	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11653589	0.84[CEU][hapmap];0.81[YRI][hapmap]
rs11654517	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11658350	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11869840	0.84[CEU][hapmap]
rs11871052	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11871364	0.86[EUR][1000 genomes]
rs12603447	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12939753	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12942936	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12949929	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12950276	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12950699	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1634260	0.89[ASN][1000 genomes]
rs197926	0.81[CEU][hapmap]
rs2007723	0.90[ASN][1000 genomes]
rs2316331	0.87[ASN][1000 genomes]
rs2317376	0.89[ASN][1000 genomes]
rs2873131	0.89[ASN][1000 genomes]
rs34038545	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34314554	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34710835	0.97[ASN][1000 genomes]
rs35721448	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851786	0.83[CEU][hapmap]
rs3851792	0.87[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap]
rs4074247	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4074249	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968253	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968286	0.84[CEU][hapmap]
rs4968301	0.81[EUR][1000 genomes]
rs4968304	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56362502	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6504622	0.84[CEU][hapmap]
rs7207418	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7214785	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7215573	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7215903	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7215907	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7219544	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7219899	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7220777	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7222781	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs736603	0.80[CEU][hapmap]
rs736604	0.81[CEU][hapmap]
rs8068715	0.84[CEU][hapmap];0.81[YRI][hapmap]
rs8077021	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9889451	0.92[ASN][1000 genomes]
rs9889762	0.84[CEU][hapmap]
rs9899078	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv522797	chr17:45084279-45183152	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	13 gene(s)	inside rSNPs	diseases
10	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	esv21010	chr17:45125753-45177221	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	esv9886	chr17:45142849-45153796	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv978431	chr17:45146826-45151336	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11079750	GOSR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45145000-45149800	Weak transcription	Spleen	Spleen
2	chr17:45145000-45150000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:45145000-45150000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:45145000-45150000	Weak transcription	Esophagus	oesophagus
5	chr17:45145000-45150000	Weak transcription	HSMM	muscle
6	chr17:45145000-45150200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr17:45145000-45150200	Weak transcription	Brain Hippocampus Middle	brain
8	chr17:45145000-45151600	Weak transcription	Psoas Muscle	Psoas
9	chr17:45145000-45152200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:45145000-45152400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:45145000-45158800	Weak transcription	NHLF	lung
12	chr17:45145000-45163600	Weak transcription	Aorta	Aorta
13	chr17:45145000-45163800	Weak transcription	Small Intestine	intestine
14	chr17:45145000-45164600	Weak transcription	Brain Angular Gyrus	brain
15	chr17:45145000-45169800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:45145000-45169800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:45145000-45169800	Weak transcription	Fetal Lung	lung
18	chr17:45145000-45176400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr17:45145000-45176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr17:45145000-45176800	Weak transcription	Lung	lung
21	chr17:45145200-45150200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:45145200-45150200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr17:45145200-45150200	Weak transcription	GM12878-XiMat	blood
24	chr17:45145200-45157400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:45145200-45158800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr17:45145200-45162200	Weak transcription	HepG2	liver
27	chr17:45145200-45169200	Weak transcription	Primary B cells from cord blood	blood
28	chr17:45145200-45170200	Weak transcription	Brain Germinal Matrix	brain
29	chr17:45145200-45176600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr17:45145400-45176000	Weak transcription	Primary T cells from cord blood	blood
31	chr17:45146000-45158600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr17:45146400-45150000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr17:45146400-45169800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr17:45146400-45170800	Weak transcription	Dnd41	blood
35	chr17:45146600-45149800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr17:45147000-45150200	Weak transcription	Fetal Muscle Leg	muscle
37	chr17:45147200-45151800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr17:45147400-45150600	Enhancers	K562	blood
39	chr17:45147400-45151200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr17:45147800-45150000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr17:45148000-45150600	Enhancers	Primary hematopoietic stem cells	blood
42	chr17:45148200-45150200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:45148200-45151800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr17:45148200-45155200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:45148400-45150000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:45148600-45149600	Enhancers	Primary T cells fromperipheralblood	blood
47	chr17:45148600-45150000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr17:45148600-45150200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr17:45148600-45150200	Genic enhancers	Fetal Intestine Small	intestine
50	chr17:45148600-45162200	Weak transcription	Stomach Mucosa	stomach

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