Variant report

Variant	rs12954256
Chromosome Location	chr18:12959059-12959060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12957784..12961031-chr18:12961742..12965819,5	K562	blood:
2	chr18:12946035..12953306-chr18:12956090..12962913,16	K562	blood:
3	chr18:12947948..12949973-chr18:12958493..12962153,3	MCF-7	breast:
4	chr18:12958261..12960549-chr18:12961742..12965129,4	K562	blood:
5	chr18:12701055..12702715-chr18:12957663..12960515,2	K562	blood:
6	chr18:12945776..12952175-chr18:12954387..12960295,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128789	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000101624	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10221326	0.92[CHB][hapmap];0.85[EUR][1000 genomes]
rs10221384	0.89[CEU][hapmap]
rs11080620	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11663049	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12605638	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12955780	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1474043	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1786263	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1787000	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1787008	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1973779	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28619103	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28641764	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2902856	0.85[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35790309	0.84[EUR][1000 genomes]
rs3809912	0.89[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs472702	0.85[CEU][hapmap]
rs472992	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs473580	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs474337	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs478006	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs498685	0.84[CEU][hapmap]
rs4995995	0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs518145	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs527839	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs554719	0.84[EUR][1000 genomes]
rs554854	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs556371	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs556536	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs562151	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs565832	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs567031	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs569453	0.83[EUR][1000 genomes]
rs570505	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs576963	0.92[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.86[MEX][hapmap]
rs578208	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6505775	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6505776	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6505777	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6505780	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs692964	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7226616	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7229870	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7233600	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7233814	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7234094	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7234960	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7237236	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7241536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7243660	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8088313	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8089123	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8097038	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8097125	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9783859	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9783903	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9948681	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9949589	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9949682	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9951698	0.81[AMR][1000 genomes]
rs9958369	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9961669	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9964466	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9965977	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12954256	CEP192	cis	Whole Blood	GTEx
rs12954256	CEP192	cis	Thyroid	GTEx
rs12954256	CEP192	cis	Esophagus Muscularis	GTEx
rs12954256	CEP192	cis	Artery Aorta	GTEx
rs12954256	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs12954256	CEP192	cis	parietal	SCAN
rs12954256	CEP192	cis	Artery Tibial	GTEx
rs12954256	CEP192	cis	Adipose Subcutaneous	GTEx
rs12954256	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs12954256	CEP192	cis	Esophagus Mucosa	GTEx
rs12954256	TUBB6	cis	lymphoblastoid	seeQTL
rs12954256	CEP192	cis	cerebellum	SCAN
rs12954256	CEP192	cis	lung	GTEx
rs12954256	SEH1L	cis	parietal	SCAN
rs12954256	CEP192	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12948800-12963200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:12948800-12963200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:12948800-12963200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr18:12948800-12963200	Weak transcription	Colon Smooth Muscle	Colon
5	chr18:12948800-12963600	Weak transcription	Esophagus	oesophagus
6	chr18:12948800-12971000	Weak transcription	Ovary	ovary
7	chr18:12948800-12971600	Weak transcription	Pancreas	Pancrea
8	chr18:12948800-12976600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr18:12948800-12989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr18:12949000-12963200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr18:12949000-12963200	Weak transcription	NHLF	lung
12	chr18:12949000-12971600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr18:12949000-12975400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr18:12949200-12960800	Weak transcription	Fetal Heart	heart
15	chr18:12949200-12960800	Weak transcription	Stomach Mucosa	stomach
16	chr18:12949200-12961000	Weak transcription	Colonic Mucosa	Colon
17	chr18:12949200-12963400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr18:12949200-12963600	Weak transcription	Small Intestine	intestine
19	chr18:12949200-12971600	Weak transcription	Brain Substantia Nigra	brain
20	chr18:12949200-12972000	Weak transcription	Right Ventricle	heart
21	chr18:12949200-12989400	Weak transcription	Psoas Muscle	Psoas
22	chr18:12949400-12963200	Weak transcription	HMEC	breast
23	chr18:12949400-12963400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr18:12950000-12969600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr18:12950000-12990200	Weak transcription	Fetal Brain Male	brain
26	chr18:12951400-12960000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr18:12951400-12963200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr18:12951400-12963200	Weak transcription	Brain Anterior Caudate	brain
29	chr18:12951400-12963200	Weak transcription	Brain Hippocampus Middle	brain
30	chr18:12951400-12971800	Weak transcription	Gastric	stomach
31	chr18:12951400-12990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr18:12951600-12963200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr18:12951600-12988200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr18:12951800-12960200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr18:12951800-12961000	Weak transcription	Spleen	Spleen
36	chr18:12951800-12963400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr18:12951800-12978400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr18:12952200-12959200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:12952400-12960600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr18:12952400-12961800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr18:12952600-12960600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr18:12953000-12960400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr18:12953000-12960600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr18:12953000-12961200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr18:12953200-12960800	Strong transcription	Liver	Liver
46	chr18:12953200-12961200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr18:12953200-12961400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr18:12953200-12962000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr18:12953200-12979000	Strong transcription	Fetal Thymus	thymus
50	chr18:12954000-12960200	Strong transcription	Fetal Muscle Leg	muscle

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