Variant report

Variant	rs2071822
Chromosome Location	chr6:36824101-36824102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36822060..36824191-chr6:36841169..36844111,2	K562	blood:
2	chr6:36769553..36772126-chr6:36822645..36824818,2	K562	blood:
3	chr6:36821600..36824429-chr6:36828707..36831696,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137168	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11751790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11751844	0.82[ASW][hapmap];0.84[CEU][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11754437	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11756425	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11758600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11758807	0.82[ASW][hapmap];0.84[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs12661551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12664239	0.83[ASN][1000 genomes]
rs2007290	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2071823	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293381	1.00[YRI][hapmap]
rs28673271	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3176344	1.00[YRI][hapmap]
rs3213536	1.00[YRI][hapmap]
rs4711470	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4711471	0.88[ASN][1000 genomes]
rs4711472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4714015	0.84[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4714019	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4714020	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs60097056	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62406642	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62406644	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6900068	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap]
rs6910582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6912602	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6912891	0.83[ASN][1000 genomes]
rs6913047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72846083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9349015	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9349017	0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9357229	0.83[ASN][1000 genomes]
rs9357230	0.84[CHB][hapmap];0.90[CHD][hapmap]
rs9368963	0.82[ASW][hapmap];0.84[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9368964	0.90[EUR][1000 genomes]
rs9368965	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380603	1.00[YRI][hapmap]
rs9380605	0.80[JPT][hapmap]
rs9380607	0.82[ASW][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9380614	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9394387	0.84[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5262	chr6:36799329-36826210	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2071822	MAPK13	cis	lymphoblastoid	seeQTL
rs2071822	C6orf125	cis	parietal	SCAN
rs2071822	SCUBE3	cis	parietal	SCAN
rs2071822	C6orf89	cis	cerebellum	SCAN
rs2071822	TCP11	cis	cerebellum	SCAN
rs2071822	C6orf89	cis	parietal	SCAN
rs2071822	LRFN2	cis	cerebellum	SCAN
rs2071822	GABRE	trans	parietal	SCAN
rs2071822	LHFPL5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36817000-36826200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:36817000-36841400	Weak transcription	Colonic Mucosa	Colon
3	chr6:36817200-36830200	Weak transcription	Fetal Lung	lung
4	chr6:36817200-36833400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:36817200-36841200	Weak transcription	Fetal Brain Male	brain
6	chr6:36817200-36842000	Weak transcription	Stomach Mucosa	stomach
7	chr6:36818000-36824800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:36819000-36830000	Weak transcription	Fetal Kidney	kidney
9	chr6:36819000-36840400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:36819400-36834000	Strong transcription	Dnd41	blood
11	chr6:36819400-36841800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:36819600-36833400	Strong transcription	Primary T cells from cord blood	blood
13	chr6:36819800-36839800	Strong transcription	Fetal Thymus	thymus
14	chr6:36820000-36824600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:36820000-36825000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:36820000-36825800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr6:36820000-36826200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:36820200-36824800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:36820200-36825000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:36820200-36825200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr6:36820200-36825800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr6:36820200-36827000	Strong transcription	Thymus	Thymus
23	chr6:36820400-36824400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:36820400-36824600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:36820400-36824600	Strong transcription	Fetal Brain Female	brain
26	chr6:36820400-36825600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:36820400-36825600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:36820400-36825600	Strong transcription	Hela-S3	cervix
29	chr6:36820400-36827000	Strong transcription	Primary hematopoietic stem cells	blood
30	chr6:36820600-36824800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:36820600-36826200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:36820600-36826800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:36820800-36825400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:36821000-36824200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:36821000-36824400	Strong transcription	Fetal Intestine Large	intestine
36	chr6:36821000-36824800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr6:36821000-36841400	Weak transcription	Small Intestine	intestine
38	chr6:36821200-36824200	Strong transcription	Brain Hippocampus Middle	brain
39	chr6:36821200-36824600	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr6:36821400-36824600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:36821600-36824200	Strong transcription	Liver	Liver
42	chr6:36821600-36824600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:36821600-36824800	Strong transcription	Primary B cells from cord blood	blood
44	chr6:36821600-36825400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:36821600-36826200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:36821600-36827000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:36821600-36827600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:36821600-36828600	Strong transcription	K562	blood
49	chr6:36821600-36830200	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:36821800-36824400	Strong transcription	HSMM	muscle

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