Variant report

Variant	rs2274200
Chromosome Location	chr6:33625696-33625697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33625658..33632208-chr6:33632440..33635133,7	MCF-7	breast:
2	chr6:33598960..33600739-chr6:33624531..33626836,2	K562	blood:
3	chr6:33623872..33628631-chr6:33630927..33635524,5	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10947420	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947421	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947422	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947423	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10947424	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947425	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11759011	1.00[MKK][hapmap]
rs12205634	1.00[CEU][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12208956	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12212284	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1570760	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229631	1.00[YRI][hapmap]
rs2274197	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713650	0.82[ASN][1000 genomes]
rs57088429	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62407633	0.83[EUR][1000 genomes]
rs62407648	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6457738	0.89[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs6932485	1.00[YRI][hapmap]
rs9348923	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357162	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9366826	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs999942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999943	0.88[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.92[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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv470811	chr6:33622933-33647651	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3435549	chr6:33624674-33628572	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv602838	chr6:33624733-33650743	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2274200	C6orf129	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33602400-33636400	Weak transcription	HSMMtube	muscle
2	chr6:33602600-33625800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:33602600-33631600	Weak transcription	Osteobl	bone
4	chr6:33603000-33628600	Weak transcription	Primary B cells from cord blood	blood
5	chr6:33603400-33626000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:33603400-33640400	Weak transcription	HUVEC	blood vessel
7	chr6:33603400-33641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:33605200-33636400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:33606600-33633000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:33606800-33626200	Weak transcription	A549	lung
11	chr6:33606800-33646600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:33608200-33640800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:33610400-33626000	Weak transcription	K562	blood
14	chr6:33611400-33626800	Weak transcription	Right Ventricle	heart
15	chr6:33611400-33643400	Weak transcription	Left Ventricle	heart
16	chr6:33613000-33659400	Strong transcription	Fetal Intestine Small	intestine
17	chr6:33613200-33660400	Strong transcription	Thymus	Thymus
18	chr6:33613400-33635400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:33613600-33635000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:33614400-33636200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr6:33615000-33660800	Strong transcription	Fetal Intestine Large	intestine
22	chr6:33615600-33626000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:33616600-33631400	Weak transcription	GM12878-XiMat	blood
24	chr6:33617200-33629200	Strong transcription	Hela-S3	cervix
25	chr6:33619000-33632800	Strong transcription	NHEK	skin
26	chr6:33619400-33629600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr6:33619600-33628400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr6:33619600-33660800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr6:33620000-33632400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:33621000-33629200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:33621000-33659400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr6:33621200-33636200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr6:33621200-33636400	Strong transcription	Primary T cells from cord blood	blood
34	chr6:33621200-33636400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:33621400-33628000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:33621400-33635800	Strong transcription	Colonic Mucosa	Colon
37	chr6:33621400-33636400	Strong transcription	Lung	lung
38	chr6:33621400-33643400	Strong transcription	Spleen	Spleen
39	chr6:33621400-33662200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:33621400-33672600	Strong transcription	Dnd41	blood
41	chr6:33622000-33660000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:33622200-33630000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:33622400-33629200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr6:33622400-33629400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:33622400-33644400	Strong transcription	Gastric	stomach
46	chr6:33622600-33628000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr6:33622800-33627400	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr6:33623000-33625800	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr6:33623000-33625800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:33623000-33627200	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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