Variant report

Variant	rs6708524
Chromosome Location	chr2:37572687-37572688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37558808..37561496-chr2:37570984..37573398,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207364	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10179447	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10196818	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10865124	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11124566	1.00[JPT][hapmap]
rs11124581	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2270331	0.94[EUR][1000 genomes]
rs2300880	0.81[TSI][hapmap]
rs2372998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2372999	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770751	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770756	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4670692	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600995	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430724	chr2:37546820-37628704	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv2685	chr2:37550096-37594923	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6708524	PRKD3	cis	parietal	SCAN
rs6708524	QPCT	cis	multi-tissue	Pritchard
rs6708524	QPCT	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37571000-37572800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:37571000-37572800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr2:37571400-37572800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr2:37571400-37572800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr2:37571400-37572800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr2:37571400-37572800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:37571400-37572800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:37571400-37572800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr2:37571400-37572800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:37571400-37572800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:37571400-37572800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
12	chr2:37571600-37572800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:37571600-37572800	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr2:37571600-37572800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:37571600-37572800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
16	chr2:37571600-37572800	Active TSS	Brain Cingulate Gyrus	brain
17	chr2:37571600-37572800	Active TSS	Brain Hippocampus Middle	brain
18	chr2:37571600-37572800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:37571600-37572800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
20	chr2:37571600-37572800	Active TSS	Rectal Smooth Muscle	rectum
21	chr2:37571600-37572800	Active TSS	Right Atrium	heart
22	chr2:37571600-37572800	Active TSS	NHDF-Ad	bronchial
23	chr2:37571600-37574600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:37571800-37572800	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr2:37571800-37572800	Active TSS	Osteobl	bone
26	chr2:37571800-37573200	Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr2:37572000-37572800	Enhancers	Fetal Brain Male	brain
28	chr2:37572000-37572800	Active TSS	HSMM	muscle
29	chr2:37572200-37572800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:37572200-37573800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:37572400-37572800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:37572400-37572800	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr2:37572400-37572800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
34	chr2:37572400-37572800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:37572400-37572800	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr2:37572400-37572800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr2:37572400-37572800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr2:37572400-37572800	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr2:37572400-37572800	Flanking Active TSS	HUVEC	blood vessel
40	chr2:37572400-37573200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:37572400-37573600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr2:37572400-37574400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:37572400-37576000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:37572400-37576200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr2:37572400-37576600	Weak transcription	Spleen	Spleen
46	chr2:37572600-37572800	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr2:37572600-37572800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr2:37572600-37572800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
49	chr2:37572600-37572800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
50	chr2:37572600-37572800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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