Variant report

Variant	rs237025
Chromosome Location	chr6:149721690-149721691
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11155639	0.82[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs11155641	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11155644	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11964335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12110411	0.81[YRI][hapmap]
rs13219868	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1446556	0.82[CEU][hapmap];0.93[CHB][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1626823	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1900300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs237010	0.88[CEU][hapmap]
rs237012	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs237016	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs237018	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs237019	0.83[CHB][hapmap];0.81[JPT][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs237024	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs237026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs237028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs237029	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs237034	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs237035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366905	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs372205	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs394563	0.86[GIH][hapmap]
rs438852	0.86[GIH][hapmap]
rs4895787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6570963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906384	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922130	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6942381	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7752555	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753269	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv969455	chr6:149720845-149727255	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs237025	SUMO4	cis	cerebellum	SCAN
rs237025	SHPRH	cis	cerebellum	SCAN
rs237025	RAET1E	cis	cerebellum	SCAN
rs237025	LRP11	cis	parietal	SCAN
rs237025	LRP11	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149687800-149726400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:149700400-149728400	Weak transcription	Hela-S3	cervix
3	chr6:149700400-149732400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:149700600-149730800	Weak transcription	Fetal Brain Male	brain
5	chr6:149700800-149732800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:149701400-149730800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:149701400-149734200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:149701600-149733600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:149703400-149730600	Weak transcription	Brain Germinal Matrix	brain
10	chr6:149703600-149730400	Weak transcription	NHLF	lung
11	chr6:149705200-149734600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:149709400-149733000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:149709600-149729800	Weak transcription	Fetal Heart	heart
14	chr6:149709600-149750200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:149711400-149726000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr6:149711400-149726600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr6:149712000-149727200	Strong transcription	Primary hematopoietic stem cells	blood
18	chr6:149713800-149735400	Weak transcription	Small Intestine	intestine
19	chr6:149714000-149728000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:149714800-149730800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:149715000-149728200	Strong transcription	Fetal Thymus	thymus
22	chr6:149715400-149732600	Strong transcription	Dnd41	blood
23	chr6:149715600-149733600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:149716000-149728000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr6:149716000-149728200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:149716400-149728600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:149716800-149725000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:149717200-149726400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:149717200-149726800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:149717400-149724200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr6:149717400-149726200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:149717400-149726200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:149717400-149726600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:149717400-149728200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:149717400-149728400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:149717400-149733200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:149717600-149722200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr6:149717600-149723600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:149717600-149724600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:149717600-149727000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:149717600-149727600	Strong transcription	Primary B cells from cord blood	blood
42	chr6:149717800-149732200	Strong transcription	GM12878-XiMat	blood
43	chr6:149718000-149722000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:149718000-149724000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:149718000-149724400	Strong transcription	Primary T cells from cord blood	blood
46	chr6:149718600-149721800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr6:149718600-149722000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr6:149718600-149722200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:149718600-149722200	Strong transcription	Fetal Intestine Large	intestine
50	chr6:149718600-149722400	Strong transcription	Placenta	Placenta

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