Variant report

Variant	rs10919260
Chromosome Location	chr1:169839595-169839596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169815997..169818292-chr1:169837214..169839882,2	K562	blood:
2	chr1:169832885..169835732-chr1:169836345..169840592,4	K562	blood:
3	chr1:169836590..169839885-chr1:169857998..169860650,3	MCF-7	breast:
4	chr1:169832885..169834948-chr1:169838301..169840592,2	K562	blood:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10159425	0.85[EUR][1000 genomes]
rs10489170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489177	1.00[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs10800477	1.00[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs10800482	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10800494	0.85[GIH][hapmap]
rs10800495	0.85[GIH][hapmap]
rs10919270	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs10919271	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs10919272	0.85[CEU][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs11804170	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs12049325	0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12123693	0.85[GIH][hapmap]
rs12128754	1.00[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.97[EUR][1000 genomes]
rs12135826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146137	0.85[GIH][hapmap]
rs12401338	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12757747	0.89[ASN][1000 genomes]
rs12760433	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1360293	0.85[GIH][hapmap]
rs2143121	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2272916	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35275808	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35688996	0.88[JPT][hapmap]
rs6427223	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6427229	0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6657512	0.85[GIH][hapmap]
rs6658548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670253	0.95[EUR][1000 genomes]
rs6679646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6688806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521273	0.88[GIH][hapmap]
rs7533194	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552710	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes]
rs882595	1.00[CEU][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9787237	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv872542	chr1:169802760-169844093	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10919260	CREG1	cis	cerebellum	SCAN
rs10919260	C1orf156	cis	cerebellum	SCAN
rs10919260	LMX1A	cis	parietal	SCAN
rs10919260	C1orf112	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169786600-169841400	Strong transcription	Dnd41	blood
3	chr1:169791200-169841200	Strong transcription	Fetal Thymus	thymus
4	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
6	chr1:169808200-169841200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:169810400-169841400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:169810600-169841200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:169810800-169841000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:169810800-169841200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:169811000-169841400	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr1:169811600-169841200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:169811800-169841400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:169812000-169840800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:169813400-169841200	Strong transcription	Fetal Intestine Large	intestine
16	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:169814600-169843200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:169814800-169848000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:169815000-169845200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr1:169815200-169843000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:169815200-169848200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:169815400-169848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:169817800-169841000	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:169817800-169848600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr1:169818000-169842800	Strong transcription	Primary B cells from cord blood	blood
26	chr1:169818200-169841200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:169818200-169847800	Strong transcription	Adipose Nuclei	Adipose
28	chr1:169819000-169848200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:169819400-169847000	Strong transcription	Liver	Liver
30	chr1:169820200-169841400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:169820400-169842600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:169820400-169844800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:169820400-169847200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:169820600-169843000	Strong transcription	Primary T cells from cord blood	blood
35	chr1:169820600-169847800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:169820600-169847800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:169820600-169848400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:169820600-169848600	Strong transcription	Fetal Lung	lung
39	chr1:169821000-169841200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:169821600-169845200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr1:169822000-169846000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:169822600-169843000	Strong transcription	Colonic Mucosa	Colon
43	chr1:169822600-169845200	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:169825600-169843000	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr1:169825600-169845800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:169826600-169841200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:169826800-169848600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:169827400-169839600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:169827400-169841200	Strong transcription	Thymus	Thymus
50	chr1:169827600-169841600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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