Variant report

Variant	rs10304
Chromosome Location	chr22:31500536-31500537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31494012..31497911-chr22:31499689..31503512,5	K562	blood:
2	chr22:31475364..31478247-chr22:31499584..31502277,3	MCF-7	breast:
3	chr22:31478371..31481367-chr22:31500336..31503939,6	K562	blood:
4	chr22:31498529..31501496-chr22:31501516..31503089,2	K562	blood:
5	chr22:31476077..31485695-chr22:31490616..31506508,29	K562	blood:
6	chr22:31482757..31485252-chr22:31500477..31503688,4	K562	blood:
7	chr22:31493570..31496471-chr22:31498580..31501028,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183963	Chromatin interaction
ENSG00000198832	Chromatin interaction
ENSG00000273387	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12484094	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2074736	1.00[YRI][hapmap]
rs2267167	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283875	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820942	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs5753454	0.91[CHB][hapmap]
rs5753458	0.91[ASN][1000 genomes]
rs5753465	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753466	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8140524	0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]

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	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv914975	chr22:31466083-31514477	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv914976	chr22:31475307-31543260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv914977	chr22:31477563-31514477	Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10304	ENSG00000183963	cis	multi-tissue	Pritchard
rs10304	MORC2	cis	parietal	SCAN
rs10304	MN1	cis	parietal	SCAN
rs10304	C22orf31	cis	cerebellum	SCAN
rs10304	INPP5J	cis	Esophagus Muscularis	GTEx
rs10304	DEAF1	trans	parietal	SCAN
rs10304	SFI1	cis	cerebellum	SCAN
rs10304	ASCC2	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31482000-31500800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr22:31482000-31501000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr22:31482000-31501200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr22:31483200-31500600	Strong transcription	HUVEC	blood vessel
5	chr22:31483200-31502000	Strong transcription	NHEK	skin
6	chr22:31484000-31502600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr22:31485200-31500800	Weak transcription	Fetal Thymus	thymus
8	chr22:31485200-31503000	Weak transcription	Fetal Kidney	kidney
9	chr22:31485800-31502800	Weak transcription	GM12878-XiMat	blood
10	chr22:31489200-31501400	Strong transcription	Gastric	stomach
11	chr22:31489600-31501600	Weak transcription	Brain Angular Gyrus	brain
12	chr22:31490800-31502000	Weak transcription	Brain Substantia Nigra	brain
13	chr22:31491000-31500600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
14	chr22:31491400-31502000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
15	chr22:31491800-31502600	Weak transcription	Liver	Liver
16	chr22:31493000-31500800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr22:31493800-31501800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr22:31494800-31501600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr22:31495200-31501800	Strong transcription	Left Ventricle	heart
20	chr22:31495400-31500800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr22:31495400-31502600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr22:31495600-31501400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr22:31495600-31501400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr22:31495800-31501000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr22:31495800-31502000	Weak transcription	Brain Anterior Caudate	brain
26	chr22:31496000-31503000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr22:31496200-31501000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr22:31496400-31502800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr22:31497200-31500800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr22:31497400-31502000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr22:31497400-31502400	Weak transcription	Small Intestine	intestine
32	chr22:31497400-31503000	Weak transcription	Dnd41	blood
33	chr22:31497800-31502600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
34	chr22:31498000-31501800	Genic enhancers	Placenta	Placenta
35	chr22:31498000-31502200	Genic enhancers	Fetal Stomach	stomach
36	chr22:31498200-31501600	Genic enhancers	Colonic Mucosa	Colon
37	chr22:31498200-31502200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr22:31498400-31501000	Weak transcription	Fetal Heart	heart
39	chr22:31498600-31501000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr22:31498600-31502200	Weak transcription	A549	lung
41	chr22:31498600-31502600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr22:31498600-31503000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:31498600-31503000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr22:31498600-31503000	Weak transcription	Thymus	Thymus
45	chr22:31498800-31500800	Weak transcription	Brain Hippocampus Middle	brain
46	chr22:31498800-31501000	Weak transcription	Fetal Brain Female	brain
47	chr22:31498800-31501800	Weak transcription	Right Atrium	heart
48	chr22:31498800-31502800	Weak transcription	Fetal Lung	lung
49	chr22:31498800-31503000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr22:31499000-31500600	Genic enhancers	Duodenum Mucosa	Duodenum

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