Variant report

Variant	rs10922244
Chromosome Location	chr1:197488569-197488570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197485830..197487622-chr1:197488513..197491078,2	MCF-7	breast:
2	chr1:197487533..197489814-chr1:197494606..197496107,2	K562	blood:
3	chr1:197487691..197489814-chr1:197493509..197496233,3	K562	blood:
4	chr1:197486893..197488949-chr1:197506821..197509108,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10494756	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10801609	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10922231	0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs10922236	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10922252	0.81[EUR][1000 genomes]
rs10922260	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1135810	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs12026564	0.81[ASN][1000 genomes]
rs12042609	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1337166	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1345529	0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs1923759	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1998711	0.81[EUR][1000 genomes]
rs2111930	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs2287537	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4026513	0.86[ASN][1000 genomes]
rs4026514	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4147323	0.85[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs4274099	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4418639	0.80[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs4604725	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs6691216	0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs7523627	0.81[EUR][1000 genomes]
rs7534863	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs927510	0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs9658810	0.81[ASN][1000 genomes]
rs9787082	0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][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	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521647	chr1:197464448-197529218	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv4010	chr1:197471463-197511397	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10922244	DENND1B	cis	parietal	SCAN
rs10922244	LHX2	trans	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197467200-197499000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:197478000-197541200	Weak transcription	Aorta	Aorta
3	chr1:197478600-197491200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:197480000-197489600	Weak transcription	Psoas Muscle	Psoas
5	chr1:197480000-197489800	Weak transcription	Brain Anterior Caudate	brain
6	chr1:197480000-197491000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:197480000-197535800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:197480200-197489200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:197480200-197541200	Weak transcription	Esophagus	oesophagus
10	chr1:197480200-197541200	Weak transcription	Fetal Thymus	thymus
11	chr1:197480400-197541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:197481000-197507000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:197481200-197491200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:197481200-197503400	Weak transcription	Primary T cells from cord blood	blood
15	chr1:197481200-197504200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:197481200-197507200	Weak transcription	Dnd41	blood
17	chr1:197481200-197508000	Weak transcription	Left Ventricle	heart
18	chr1:197481200-197513400	Weak transcription	Adipose Nuclei	Adipose
19	chr1:197481400-197503600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:197481400-197529600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:197482000-197508000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:197482000-197508000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:197482200-197491000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:197482200-197495200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:197482200-197507600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:197482200-197507800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr1:197487200-197489400	Weak transcription	Fetal Brain Male	brain
28	chr1:197487800-197488600	Enhancers	Fetal Heart	heart
29	chr1:197487800-197490000	Weak transcription	Ovary	ovary
30	chr1:197487800-197536000	Weak transcription	Fetal Lung	lung
31	chr1:197488000-197489600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:197488200-197489600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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