Variant report

Variant	rs12205634
Chromosome Location	chr6:33611667-33611668
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33611230..33613955-chr6:33617910..33620269,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10947420	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10947421	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10947422	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10947423	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947424	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10947425	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11759011	0.89[JPT][hapmap];1.00[MKK][hapmap]
rs12190817	0.86[AFR][1000 genomes]
rs12208956	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12212284	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1570760	0.94[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]
rs2147658	0.86[CHB][hapmap]
rs2274197	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]
rs2274200	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]
rs3748079	1.00[ASW][hapmap];0.86[AFR][1000 genomes]
rs57088429	0.82[EUR][1000 genomes]
rs62407633	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62407648	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72882008	0.86[AFR][1000 genomes]
rs9348923	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9357162	1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9366826	1.00[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs942636	0.89[JPT][hapmap]
rs9469525	0.86[AFR][1000 genomes]
rs999942	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs999943	0.88[CEU][hapmap];0.80[GIH][hapmap]

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	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	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
3	esv1817557	chr6:33584788-33614127	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv1813933	chr6:33587443-33614127	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12205634	C6orf129	cis	cerebellum	SCAN
rs12205634	PIM1	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33602400-33617800	Weak transcription	NHLF	lung
2	chr6:33602400-33622600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:33602400-33636400	Weak transcription	HSMMtube	muscle
4	chr6:33602600-33614800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:33602600-33619200	Weak transcription	NHDF-Ad	bronchial
6	chr6:33602600-33623400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:33602600-33624400	Weak transcription	Small Intestine	intestine
8	chr6:33602600-33625400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:33602600-33625800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:33602600-33631600	Weak transcription	Osteobl	bone
11	chr6:33602800-33613400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:33602800-33624400	Weak transcription	Pancreas	Pancrea
13	chr6:33603000-33624000	Weak transcription	HSMM	muscle
14	chr6:33603000-33628600	Weak transcription	Primary B cells from cord blood	blood
15	chr6:33603200-33619600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:33603400-33623000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:33603400-33626000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:33603400-33640400	Weak transcription	HUVEC	blood vessel
19	chr6:33603400-33641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:33604400-33614400	Weak transcription	HepG2	liver
21	chr6:33604800-33623000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:33604800-33623400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:33605000-33624400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:33605000-33625400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:33605200-33624000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:33605200-33624400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:33605200-33636400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:33606400-33613200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:33606600-33633000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:33606800-33626200	Weak transcription	A549	lung
31	chr6:33606800-33646600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:33607600-33612400	Strong transcription	Primary T cells from cord blood	blood
33	chr6:33607800-33611800	Genic enhancers	Spleen	Spleen
34	chr6:33608200-33611800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:33608200-33611800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:33608200-33640800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:33608400-33612000	Strong transcription	Lung	lung
38	chr6:33608600-33611800	Strong transcription	Dnd41	blood
39	chr6:33608600-33612200	Strong transcription	Fetal Intestine Small	intestine
40	chr6:33609200-33616400	Weak transcription	Fetal Thymus	thymus
41	chr6:33609600-33623600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr6:33609800-33613200	Weak transcription	GM12878-XiMat	blood
43	chr6:33609800-33619400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr6:33610000-33615000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:33610200-33615000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:33610200-33615000	Weak transcription	HMEC	breast
47	chr6:33610400-33623600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:33610400-33624000	Weak transcription	Fetal Lung	lung
49	chr6:33610400-33624000	Weak transcription	Stomach Mucosa	stomach
50	chr6:33610400-33626000	Weak transcription	K562	blood

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