Variant report

Variant	rs12602291
Chromosome Location	chr17:15869071-15869072
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	chr17:15866407..15869569-chr17:15884863..15887251,3	K562	blood:
2	chr17:15860784..15862668-chr17:15867479..15869134,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1076423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1076424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078322	0.87[ASN][1000 genomes]
rs11871230	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11871236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16959491	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16959521	0.87[ASN][1000 genomes]
rs17715109	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3826361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4791659	0.87[ASN][1000 genomes]
rs4792714	0.87[ASN][1000 genomes]
rs56060666	0.83[ASN][1000 genomes]
rs56250180	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56258621	0.87[ASN][1000 genomes]
rs59749475	0.87[ASN][1000 genomes]
rs60198485	0.91[EUR][1000 genomes]
rs61365058	0.91[EUR][1000 genomes]
rs61530520	0.91[EUR][1000 genomes]
rs6502476	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6502477	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6502483	0.85[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs6502486	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6502487	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs7209240	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7212804	0.87[ASN][1000 genomes]
rs7213125	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7218471	1.00[EUR][1000 genomes]
rs7220790	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs73978569	1.00[EUR][1000 genomes]
rs73978571	1.00[EUR][1000 genomes]
rs73978572	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73978592	0.87[ASN][1000 genomes]
rs73978593	0.83[ASN][1000 genomes]
rs73978596	0.87[ASN][1000 genomes]
rs8073693	0.87[ASN][1000 genomes]
rs8074888	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs8077373	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs8077643	0.91[EUR][1000 genomes]
rs8079763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	nsv1062951	chr17:15561070-15890644	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1066023	chr17:15607267-16053512	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
5	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv1061222	chr17:15672934-15999778	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv907706	chr17:15731923-16056442	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1067555	chr17:15804228-16001117	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
10	nsv907707	chr17:15846535-15950751	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv907709	chr17:15851196-15937487	Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	nsv907708	chr17:15851196-15950751	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv1057493	chr17:15852125-15930718	Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv543215	chr17:15852125-15930718	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv907710	chr17:15854257-15950751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12602291	Hs.379903	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15851200-15869600	Weak transcription	Gastric	stomach
2	chr17:15855800-15869800	Weak transcription	Fetal Intestine Small	intestine
3	chr17:15862400-15869800	Weak transcription	Spleen	Spleen
4	chr17:15862600-15869800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr17:15863000-15869200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:15863400-15869400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr17:15863400-15869800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr17:15866200-15869800	Enhancers	HMEC	breast
9	chr17:15866400-15871800	Enhancers	NH-A	brain
10	chr17:15866600-15871200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:15867400-15869600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr17:15867400-15869600	Weak transcription	NHLF	lung
13	chr17:15867400-15878000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:15867600-15869600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:15867600-15869800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:15868200-15869200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr17:15868200-15869600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr17:15868200-15870200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:15868200-15870200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr17:15868200-15870400	Enhancers	A549	lung
21	chr17:15868200-15870400	Enhancers	Osteobl	bone
22	chr17:15868400-15869200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr17:15868400-15869200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr17:15868400-15869600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:15868400-15869600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr17:15868400-15869800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr17:15868400-15869800	Enhancers	HUVEC	blood vessel
28	chr17:15868400-15870000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr17:15868400-15870000	Enhancers	Thymus	Thymus
30	chr17:15868400-15870600	Enhancers	HSMM	muscle
31	chr17:15868400-15871400	Enhancers	Hela-S3	cervix
32	chr17:15868400-15871400	Enhancers	NHDF-Ad	bronchial
33	chr17:15868400-15871600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr17:15868600-15869400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr17:15868600-15869400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr17:15868600-15869400	Enhancers	Primary T cells from cord blood	blood
37	chr17:15868600-15869400	Enhancers	Lung	lung
38	chr17:15868600-15869600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:15868600-15869600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr17:15868600-15869600	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr17:15868600-15869800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr17:15868600-15869800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr17:15868600-15870000	Enhancers	Brain Anterior Caudate	brain
44	chr17:15868600-15870000	Enhancers	Brain Germinal Matrix	brain
45	chr17:15868600-15870200	Enhancers	Fetal Heart	heart
46	chr17:15868600-15870400	Enhancers	Fetal Lung	lung
47	chr17:15868600-15870400	Enhancers	HSMMtube	muscle
48	chr17:15868600-15870600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr17:15868600-15870600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr17:15868600-15870600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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