Variant report

Variant	rs9370236
Chromosome Location	chr6:53724274-53724275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53719967..53722619-chr6:53723859..53726928,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs13197492	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3000998	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3001003	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3003496	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3003497	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4077760	0.85[CHB][hapmap]
rs4269375	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4276503	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4342426	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4475321	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4476827	0.85[CHB][hapmap]
rs4493745	0.86[TSI][hapmap]
rs4587161	0.88[EUR][1000 genomes]
rs4715425	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5001609	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458960	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6458970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6900929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905927	0.85[CHB][hapmap]
rs6934444	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7767443	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9349686	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9357774	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9357775	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9367542	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382239	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9370236	PRIM2	cis	parietal	SCAN
rs9370236	LRRC1	cis	parietal	SCAN
rs9370236	C6orf142	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
3	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
5	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:53719800-53727600	Enhancers	Brain Substantia Nigra	brain
7	chr6:53719800-53727800	Enhancers	Brain Hippocampus Middle	brain
8	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
9	chr6:53720000-53724400	Enhancers	Brain Anterior Caudate	brain
10	chr6:53720000-53727600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:53720600-53741400	Weak transcription	Dnd41	blood
12	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
13	chr6:53721200-53726200	Weak transcription	Fetal Intestine Small	intestine
14	chr6:53721200-53726400	Weak transcription	Fetal Intestine Large	intestine
15	chr6:53721200-53726600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:53721200-53726800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:53721600-53728000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:53721800-53725600	Weak transcription	Aorta	Aorta
19	chr6:53721800-53726800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:53722000-53725000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:53722400-53724400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr6:53722400-53725400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:53722600-53725000	Enhancers	HUVEC	blood vessel
25	chr6:53722600-53725400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:53722600-53725600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:53722600-53725600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:53722800-53726200	Weak transcription	HepG2	liver
29	chr6:53722800-53726400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:53723000-53725400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:53723000-53725600	Weak transcription	Lung	lung
32	chr6:53723000-53726200	Weak transcription	HSMMtube	muscle
33	chr6:53723000-53727000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:53723000-53727200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:53723000-53727200	Enhancers	Brain Angular Gyrus	brain
36	chr6:53723000-53728000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:53723000-53728000	Weak transcription	Pancreas	Pancrea
38	chr6:53723000-53728000	Weak transcription	Right Atrium	heart
39	chr6:53723200-53725400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:53723200-53725600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:53723200-53725600	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:53723200-53725800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:53723400-53726000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:53723400-53726000	Weak transcription	HMEC	breast
45	chr6:53723400-53726000	Weak transcription	NHEK	skin
46	chr6:53723400-53726400	Weak transcription	Esophagus	oesophagus
47	chr6:53723400-53736800	Weak transcription	Stomach Mucosa	stomach
48	chr6:53724000-53724600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:53724000-53724600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:53724000-53725000	Weak transcription	Brain Cingulate Gyrus	brain

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