Variant report

Variant	rs12945855
Chromosome Location	chr17:16139149-16139150
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	chr17:16133803..16136363-chr17:16137901..16140091,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1029809	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1065822	0.81[CEU][hapmap]
rs1079533	0.81[CEU][hapmap]
rs10852834	0.91[EUR][1000 genomes]
rs11078337	0.84[EUR][1000 genomes]
rs1125156	0.81[CEU][hapmap]
rs1160109	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap]
rs11650283	0.83[TSI][hapmap]
rs11650427	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650678	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap]
rs11650956	0.83[EUR][1000 genomes]
rs11651290	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs11651578	0.86[EUR][1000 genomes]
rs11653500	0.81[EUR][1000 genomes]
rs11653650	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654658	0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs11656811	0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11868284	0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11872032	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap]
rs12150564	0.91[EUR][1000 genomes]
rs12936233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936529	0.91[EUR][1000 genomes]
rs12938397	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs12938878	0.82[EUR][1000 genomes]
rs12939078	0.83[EUR][1000 genomes]
rs12946619	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1476810	0.83[TSI][hapmap]
rs15739	0.83[TSI][hapmap]
rs178657	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[TSI][hapmap]
rs178785	0.81[EUR][1000 genomes]
rs178787	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs178789	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs178790	0.84[AFR][1000 genomes]
rs178791	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs178792	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs178793	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs178795	0.84[AFR][1000 genomes]
rs178796	0.85[AFR][1000 genomes]
rs178797	0.85[CEU][hapmap];0.85[CHB][hapmap];0.83[TSI][hapmap]
rs178798	0.81[CEU][hapmap];0.85[CHB][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs178799	0.81[CEU][hapmap]
rs178802	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs178805	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs178809	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs178816	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs178820	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[TSI][hapmap]
rs178837	0.81[TSI][hapmap]
rs1963811	0.85[EUR][1000 genomes]
rs1989856	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[TSI][hapmap]
rs2109262	0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs2324306	0.83[EUR][1000 genomes]
rs2324307	0.84[EUR][1000 genomes]
rs34331598	0.82[EUR][1000 genomes]
rs3785622	0.83[EUR][1000 genomes]
rs3785625	0.86[EUR][1000 genomes]
rs3785626	0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs3785631	0.81[CEU][hapmap]
rs3815039	0.81[CEU][hapmap]
rs4470185	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4791662	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap]
rs4792728	0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs4792729	0.86[EUR][1000 genomes]
rs4792731	0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs62072527	0.81[EUR][1000 genomes]
rs62072528	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502498	0.81[EUR][1000 genomes]
rs7210990	0.84[CEU][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes]
rs7215071	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223428	0.81[EUR][1000 genomes]
rs8074727	0.85[EUR][1000 genomes]
rs9889720	0.83[ASN][1000 genomes]
rs9891379	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs9897073	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9902141	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[TSI][hapmap]
rs9903464	1.00[CHB][hapmap];0.81[TSI][hapmap]
rs9903871	0.80[ASN][1000 genomes]
rs9909022	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9909697	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs9910148	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs9914734	0.86[EUR][1000 genomes]
rs9916220	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944524	0.91[TSI][hapmap];0.84[EUR][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	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	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
3	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
4	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
5	nsv522169	chr17:15923709-16147821	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv907715	chr17:16019978-16206540	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
7	nsv907717	chr17:16076898-16239832	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
8	nsv907718	chr17:16080849-16143709	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	nsv528263	chr17:16097430-16196996	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
10	esv3326983	chr17:16138963-16210147	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12945855	CENPV	cis	lymphoblastoid	seeQTL
rs12945855	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs12945855	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs12945855	TTC19	cis	lymphoblastoid	seeQTL
rs12945855	PRR6	cis	multi-tissue	Pritchard
rs12945855	LOC125150	cis	uninvolved skin	skin_eQTL
rs12945855	CENPV	cis	Artery Tibial	GTEx
rs12945855	ADORA2B	cis	Thyroid	GTEx
rs12945855	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs12945855	LOC125150	cis	normal skin	skin_eQTL
rs12945855	ADORA2B	cis	Artery Tibial	GTEx
rs12945855	ADORA2B	cis	Esophagus Muscularis	GTEx
rs12945855	ADORA2B	cis	Nerve Tibial	GTEx
rs12945855	ADORA2B	cis	Muscle Skeletal	GTEx
rs12945855	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs12945855	ZSWIM7	cis	Muscle Skeletal	GTEx
rs12945855	LOC125150	cis	lesional skin	skin_eQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16121000-16163200	Weak transcription	Spleen	Spleen
2	chr17:16121200-16141400	Weak transcription	Brain Substantia Nigra	brain
3	chr17:16121200-16142800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:16121200-16157000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:16121200-16158800	Weak transcription	Left Ventricle	heart
6	chr17:16121200-16159800	Weak transcription	Lung	lung
7	chr17:16121200-16163000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:16121400-16140200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr17:16121400-16140400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:16121400-16141400	Weak transcription	Colon Smooth Muscle	Colon
11	chr17:16121400-16158600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr17:16121400-16158800	Weak transcription	Fetal Muscle Leg	muscle
13	chr17:16121400-16159000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr17:16121400-16170600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:16121600-16139200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr17:16121600-16139400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr17:16121600-16143000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:16121600-16143000	Weak transcription	Fetal Lung	lung
19	chr17:16121600-16147000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr17:16121600-16150200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr17:16121600-16151800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr17:16121600-16158400	Weak transcription	Brain Hippocampus Middle	brain
23	chr17:16121600-16158600	Weak transcription	Brain Germinal Matrix	brain
24	chr17:16121800-16139200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:16121800-16146600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr17:16121800-16150200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr17:16121800-16153600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:16121800-16158200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr17:16121800-16158400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr17:16121800-16163200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr17:16121800-16163200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:16122000-16163400	Weak transcription	Fetal Brain Female	brain
33	chr17:16122200-16146800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr17:16122200-16150200	Weak transcription	Liver	Liver
35	chr17:16122400-16139400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:16123000-16154200	Weak transcription	Ovary	ovary
37	chr17:16124200-16158200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:16126200-16163200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr17:16126200-16163400	Weak transcription	Primary B cells from cord blood	blood
40	chr17:16126400-16158800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr17:16126600-16153800	Weak transcription	A549	lung
42	chr17:16127000-16140200	Weak transcription	Fetal Stomach	stomach
43	chr17:16127600-16158600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr17:16127800-16147000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr17:16130400-16146000	Weak transcription	K562	blood
46	chr17:16130400-16147000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr17:16132200-16140800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr17:16132200-16163200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:16132400-16144800	Weak transcription	HepG2	liver
50	chr17:16132400-16163600	Weak transcription	HSMM	muscle

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