Variant report

Variant	rs2274197
Chromosome Location	chr6:33645115-33645116
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33638337..33641498-chr6:33643269..33645828,4	K562	blood:
2	chr6:33644740..33654543-chr6:33656969..33664772,16	MCF-7	breast:
3	chr6:33640895..33643218-chr6:33644237..33647078,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269490	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10947420	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10947421	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10947422	0.94[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10947423	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10947424	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10947425	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11759011	1.00[MKK][hapmap]
rs12205634	0.94[CEU][hapmap];0.81[GIH][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12208956	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12212284	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1536036	0.81[CHD][hapmap]
rs1570760	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[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];0.81[ASN][1000 genomes]
rs2229631	1.00[YRI][hapmap]
rs2274200	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]
rs57088429	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62407648	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6457738	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs6932485	1.00[YRI][hapmap]
rs9348923	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9357162	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9366826	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs999942	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs999943	0.83[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	nsv885771	chr6:33626717-33660143	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv522906	chr6:33638180-33647651	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2274197	C6orf129	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33606800-33646600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:33613000-33659400	Strong transcription	Fetal Intestine Small	intestine
3	chr6:33613200-33660400	Strong transcription	Thymus	Thymus
4	chr6:33615000-33660800	Strong transcription	Fetal Intestine Large	intestine
5	chr6:33619600-33660800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr6:33621000-33659400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr6:33621400-33662200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:33621400-33672600	Strong transcription	Dnd41	blood
9	chr6:33622000-33660000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:33623200-33649000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:33625200-33645200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:33629000-33662800	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:33630200-33651000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:33630400-33650800	Weak transcription	Ovary	ovary
16	chr6:33630400-33660800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr6:33630600-33645800	Strong transcription	Fetal Thymus	thymus
18	chr6:33631600-33667000	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr6:33631800-33649400	Strong transcription	Pancreas	Pancrea
20	chr6:33631800-33661200	Weak transcription	Liver	Liver
21	chr6:33636600-33660600	Strong transcription	Colonic Mucosa	Colon
22	chr6:33636800-33660200	Strong transcription	Lung	lung
23	chr6:33636800-33661400	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:33637000-33650000	Strong transcription	Primary T cells from cord blood	blood
25	chr6:33637200-33650400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:33637200-33650400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:33637400-33650400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:33637400-33661600	Strong transcription	Esophagus	oesophagus
29	chr6:33637600-33646400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr6:33637600-33647000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:33637600-33650000	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:33637600-33650200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr6:33637800-33650000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:33637800-33650400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:33638000-33652200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr6:33638200-33659200	Weak transcription	Right Atrium	heart
37	chr6:33638800-33645400	Weak transcription	HepG2	liver
38	chr6:33638800-33650800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:33639200-33645600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:33639400-33646000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:33639600-33659200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:33641000-33646000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:33641000-33646000	Genic enhancers	NHDF-Ad	bronchial
45	chr6:33641000-33647000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:33641000-33650600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:33641200-33646000	Strong transcription	Primary B cells from cord blood	blood
49	chr6:33641200-33646000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr6:33641200-33648600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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