Variant report

Variant	rs12327306
Chromosome Location	chr18:13130681-13130682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:13124233..13126010-chr18:13129729..13132355,2	K562	blood:
2	chr18:13130413..13132086-chr18:13135033..13137817,2	MCF-7	breast:
3	chr18:13129145..13130942-chr18:13543662..13545815,2	MCF-7	breast:
4	chr18:13128234..13129969-chr18:13130472..13133331,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10163827	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11080617	0.91[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap]
rs11080618	0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap]
rs11659979	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11661559	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11661908	0.81[TSI][hapmap]
rs11662634	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11664213	0.83[EUR][1000 genomes]
rs11664469	1.00[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12326275	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12607919	0.85[CHD][hapmap]
rs12953783	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12957380	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12960349	0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs12970508	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs12971036	0.82[CHB][hapmap]
rs13381134	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13381779	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17603207	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17659689	0.85[CHD][hapmap]
rs17659896	1.00[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1786978	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1893323	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2282540	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282541	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28654613	0.90[EUR][1000 genomes]
rs34003232	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34117444	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34302481	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35563947	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3976787	0.85[CHD][hapmap]
rs489480	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs496270	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518227	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71353241	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7228684	0.95[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7234938	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7236710	0.91[EUR][1000 genomes]
rs8090667	0.85[CHD][hapmap]
rs8093236	0.85[CHD][hapmap]
rs8566	0.86[AMR][1000 genomes];0.83[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	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv515878	chr18:13122618-13142415	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv817785	chr18:13130681-13133577	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12327306	CEP192	cis	Thyroid	GTEx
rs12327306	CEP192	cis	Artery Tibial	GTEx
rs12327306	CEP192	cis	multi-tissue	Pritchard
rs12327306	CEP192	cis	parietal	SCAN
rs12327306	CEP192	cis	cerebellum	SCAN
rs12327306	CEP192	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13106800-13135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:13118200-13132600	Weak transcription	HepG2	liver
3	chr18:13118400-13135600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr18:13118400-13136200	Weak transcription	Psoas Muscle	Psoas
5	chr18:13118800-13136800	Weak transcription	HSMMtube	muscle
6	chr18:13119000-13130800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr18:13119000-13133400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr18:13119000-13134200	Weak transcription	Fetal Lung	lung
9	chr18:13119000-13136400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr18:13119200-13135800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr18:13119200-13136400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr18:13119400-13133600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr18:13119600-13135400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr18:13121200-13136400	Weak transcription	NHDF-Ad	bronchial
15	chr18:13121400-13134000	Weak transcription	HMEC	breast
16	chr18:13121400-13136600	Weak transcription	Brain Angular Gyrus	brain
17	chr18:13121600-13131600	Weak transcription	Fetal Kidney	kidney
18	chr18:13121600-13135800	Weak transcription	Fetal Brain Male	brain
19	chr18:13121600-13136000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr18:13121800-13134200	Weak transcription	HUVEC	blood vessel
21	chr18:13121800-13136400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr18:13122000-13136400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr18:13123800-13136400	Weak transcription	HSMM	muscle
24	chr18:13124800-13131400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr18:13125400-13130800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr18:13125600-13135800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr18:13126200-13130800	Strong transcription	Fetal Stomach	stomach
28	chr18:13126400-13130800	Strong transcription	Fetal Intestine Small	intestine
29	chr18:13126600-13135000	Weak transcription	Ovary	ovary
30	chr18:13126800-13131200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr18:13126800-13133400	Weak transcription	K562	blood
32	chr18:13127000-13133400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr18:13127000-13135200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr18:13127000-13136200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr18:13127000-13136200	Weak transcription	Placenta	Placenta
36	chr18:13127200-13130800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr18:13127200-13135800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr18:13127200-13136200	Weak transcription	Brain Anterior Caudate	brain
39	chr18:13127400-13132000	Weak transcription	Fetal Intestine Large	intestine
40	chr18:13127400-13132000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr18:13127400-13134200	Weak transcription	NHEK	skin
42	chr18:13127400-13135600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr18:13127400-13135800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr18:13127400-13135800	Weak transcription	GM12878-XiMat	blood
45	chr18:13127400-13136400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr18:13127600-13131200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr18:13127600-13132400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr18:13127600-13132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr18:13127600-13133200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr18:13127600-13134800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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