Variant report

Variant	rs6806706
Chromosome Location	chr3:43066308-43066309
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43059886..43061659-chr3:43065331..43067767,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13061038	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13095711	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2936817	1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3732856	0.92[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs476336	0.87[EUR][1000 genomes]
rs496436	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs509527	0.87[EUR][1000 genomes]
rs517650	0.89[CEU][hapmap];0.89[GIH][hapmap];0.86[EUR][1000 genomes]
rs536572	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs541007	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs56009835	0.80[ASN][1000 genomes]
rs565521	0.89[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs590899	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs606724	0.87[EUR][1000 genomes]
rs62247065	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643663	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs648273	0.80[ASN][1000 genomes]
rs658958	1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs660324	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs664628	0.92[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs693290	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs697327	1.00[CEU][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs704912	0.92[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs834178	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs834188	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs834191	0.87[EUR][1000 genomes]
rs870238	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311333	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9882262	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv432417	chr3:43045796-43098296	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6806706	C3orf39	cis	parietal	SCAN
rs6806706	CCR9	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43053600-43073200	Weak transcription	Right Atrium	heart
2	chr3:43059600-43074400	Weak transcription	Lung	lung
3	chr3:43059600-43084600	Weak transcription	Pancreas	Pancrea
4	chr3:43060800-43069600	Weak transcription	Stomach Mucosa	stomach
5	chr3:43061000-43072200	Weak transcription	Liver	Liver
6	chr3:43061000-43080200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:43061800-43073000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:43063000-43077400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:43063400-43072000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:43063600-43072600	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:43063600-43084800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:43064000-43077800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:43064400-43066600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:43064600-43066400	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr3:43064600-43066400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr3:43064600-43066600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:43064600-43066600	Flanking Active TSS	Dnd41	blood
18	chr3:43064600-43066800	Enhancers	Primary hematopoietic stem cells	blood
19	chr3:43064800-43066400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr3:43064800-43066400	Enhancers	Adipose Nuclei	Adipose
21	chr3:43064800-43067400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:43065000-43066400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:43065000-43066400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:43065000-43067200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:43065200-43066400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:43065200-43067000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:43065200-43067000	Enhancers	Fetal Intestine Small	intestine
28	chr3:43065200-43072400	Weak transcription	Placenta	Placenta
29	chr3:43065400-43067000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:43065400-43084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:43065600-43066400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:43065800-43067000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr3:43065800-43067400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:43065800-43067800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr3:43065800-43067800	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr3:43066000-43066400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:43066000-43066400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr3:43066000-43066400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:43066000-43066600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr3:43066000-43066800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:43066000-43067200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr3:43066000-43068000	Enhancers	Fetal Thymus	thymus
43	chr3:43066200-43066600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:43066200-43067000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr3:43066200-43067800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:43066200-43068000	Enhancers	Thymus	Thymus
47	chr3:43066200-43068200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:43066200-43068200	Enhancers	Primary T helper cells PMA-I stimulated	--

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