Variant report

Variant	rs9302899
Chromosome Location	chr17:67315048-67315049
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	chr17:67314877..67316596-chr17:73774432..73776155,2	MCF-7	breast:
2	chr17:67302738..67306142-chr17:67312679..67315678,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP2K6-7	chr17:67314874-67315102	NONHSAT055578

Variant related genes	Relation type
ENSG00000132475	Chromatin interaction
ENSG00000154265	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1476749	0.87[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs16973883	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16973905	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17776943	1.00[GIH][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs28496489	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28592152	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4553686	0.94[EUR][1000 genomes]
rs4968854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58324131	0.81[AMR][1000 genomes]
rs7208451	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes]
rs7225918	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73998226	0.80[EUR][1000 genomes]
rs9889277	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9895649	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap]
rs9908248	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9910364	0.94[EUR][1000 genomes]
rs9912665	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv457889	chr17:67210992-67332355	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
3	nsv575934	chr17:67210992-67332355	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
4	nsv833527	chr17:67240575-67400871	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv575935	chr17:67256162-67327806	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
6	nsv457890	chr17:67264339-67327806	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
7	nsv575936	chr17:67264339-67327806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
8	nsv908706	chr17:67290840-67332355	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
9	nsv575937	chr17:67304447-67327806	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
10	nsv962365	chr17:67314651-67315431	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9302899	ABCA10	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67244000-67321800	Weak transcription	Right Ventricle	heart
2	chr17:67261400-67322000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:67285000-67316200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr17:67290000-67317400	Weak transcription	Gastric	stomach
5	chr17:67290200-67319600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:67291800-67321800	Weak transcription	Esophagus	oesophagus
7	chr17:67293200-67315600	Weak transcription	GM12878-XiMat	blood
8	chr17:67297000-67319400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr17:67297000-67321800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr17:67304200-67321800	Weak transcription	HUVEC	blood vessel
11	chr17:67305200-67321600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:67306000-67321800	Weak transcription	Placenta	Placenta
13	chr17:67306400-67321000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr17:67306600-67319600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:67307000-67321800	Weak transcription	Left Ventricle	heart
16	chr17:67307000-67321800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr17:67307200-67318800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr17:67307200-67319000	Weak transcription	Fetal Intestine Large	intestine
19	chr17:67307200-67321800	Weak transcription	Thymus	Thymus
20	chr17:67307600-67316000	Weak transcription	NHDF-Ad	bronchial
21	chr17:67308000-67321200	Weak transcription	Fetal Intestine Small	intestine
22	chr17:67310200-67321000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr17:67310800-67316200	Weak transcription	Osteobl	bone
24	chr17:67311000-67315200	Weak transcription	Liver	Liver
25	chr17:67311000-67315600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:67311000-67315800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr17:67311000-67316400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:67311000-67322000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:67311200-67315800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr17:67311200-67319000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr17:67311200-67319400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr17:67311200-67320400	Weak transcription	Pancreas	Pancrea
33	chr17:67311200-67320400	Weak transcription	Psoas Muscle	Psoas
34	chr17:67311200-67321800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr17:67311200-67322000	Weak transcription	Brain Anterior Caudate	brain
36	chr17:67311400-67316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr17:67311400-67319200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr17:67313800-67319200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:67314000-67320400	Weak transcription	HMEC	breast
40	chr17:67314000-67321600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr17:67314200-67321600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr17:67315000-67315800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr17:67315000-67316800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr17:67315000-67317000	Enhancers	Pancreatic Islets	Pancreatic Islet

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