Variant report

Variant	rs12457771
Chromosome Location	chr18:12677934-12677935
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	chr18:12375835..12378198-chr18:12677932..12680535,3	K562	blood:
2	chr18:12677577..12680065-chr18:12699898..12703044,3	K562	blood:

Variant related genes	Relation type
ENSG00000101624	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1062235	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs1129214	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs11874852	0.83[CEU][hapmap]
rs12373207	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12373259	0.91[ASN][1000 genomes]
rs12454322	0.84[EUR][1000 genomes]
rs12455268	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12455295	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457026	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap]
rs12458097	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12458895	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12954079	0.92[ASN][1000 genomes]
rs12957555	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957603	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957810	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12960623	0.94[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs12960997	0.92[ASN][1000 genomes]
rs12962598	0.92[ASN][1000 genomes]
rs12963505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964507	0.91[ASN][1000 genomes]
rs12965733	0.87[ASN][1000 genomes]
rs12965990	0.92[ASN][1000 genomes]
rs12966246	0.86[ASN][1000 genomes]
rs12966367	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966424	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12968771	0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12969300	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12969446	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12969938	0.92[ASN][1000 genomes]
rs12971256	0.87[ASN][1000 genomes]
rs1362709	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1549011	0.94[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs1592642	0.87[ASN][1000 genomes]
rs1592643	0.88[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs17616402	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971702	0.86[ASN][1000 genomes]
rs2011575	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011579	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051262	0.91[ASN][1000 genomes]
rs2302768	0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs28820339	0.87[ASN][1000 genomes]
rs28832066	0.92[ASN][1000 genomes]
rs34040888	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34120824	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34277169	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34472716	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34537593	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34632667	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34690304	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34847769	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35322088	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35506854	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35634465	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35699948	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35898717	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809919	0.91[ASN][1000 genomes]
rs3902981	0.94[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4296322	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs45589535	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45596833	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4633785	0.94[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs55870255	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62095975	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096023	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096046	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62096048	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505760	0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs66808227	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7229168	0.86[CEU][hapmap];0.91[JPT][hapmap]
rs7233175	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7233694	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7507018	0.92[ASN][1000 genomes]
rs8083182	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8083217	0.82[ASN][1000 genomes]
rs8086099	0.87[ASN][1000 genomes]
rs8086265	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8086846	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8097134	0.87[ASN][1000 genomes]
rs9303774	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9303775	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9303776	0.89[ASN][1000 genomes]
rs933600	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948319	0.93[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs963920	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9945140	0.92[ASN][1000 genomes]
rs9945644	0.92[ASN][1000 genomes]
rs9945801	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9948844	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9949293	0.92[ASN][1000 genomes]
rs9950365	0.92[ASN][1000 genomes]
rs9951576	0.92[ASN][1000 genomes]
rs9952000	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9954112	0.92[ASN][1000 genomes]
rs9955985	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9957880	0.91[ASN][1000 genomes]
rs9958100	0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs9958412	0.92[ASN][1000 genomes]
rs9959039	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959458	0.92[ASN][1000 genomes]
rs9959536	0.91[ASN][1000 genomes]
rs9960555	0.91[ASN][1000 genomes]
rs9961799	0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9962006	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9963809	0.88[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9964868	0.94[ASN][1000 genomes]
rs9966464	0.90[ASN][1000 genomes]
rs9966490	0.91[ASN][1000 genomes]
rs9966672	0.91[ASN][1000 genomes]
rs9967437	0.92[ASN][1000 genomes]
rs9967553	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12457771	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs12457771	TNFSF5IP1	Cis_1M	lymphoblastoid	RTeQTL
rs12457771	SPIRE1	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12658800-12679200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:12658800-12701800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr18:12659000-12679200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr18:12659000-12679200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr18:12659000-12679400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr18:12659000-12700200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr18:12659800-12679200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr18:12660000-12692600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr18:12660400-12679000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr18:12660400-12700800	Weak transcription	Fetal Brain Male	brain
11	chr18:12661000-12679000	Weak transcription	HUVEC	blood vessel
12	chr18:12662800-12701600	Weak transcription	Aorta	Aorta
13	chr18:12664800-12679000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:12665800-12684200	Weak transcription	Pancreas	Pancrea
15	chr18:12667000-12701600	Weak transcription	Gastric	stomach
16	chr18:12667800-12679000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr18:12668400-12679200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr18:12668400-12694800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr18:12668600-12685800	Weak transcription	Brain Hippocampus Middle	brain
20	chr18:12669200-12694200	Weak transcription	A549	lung
21	chr18:12669800-12694200	Weak transcription	Hela-S3	cervix
22	chr18:12670000-12679200	Weak transcription	Esophagus	oesophagus
23	chr18:12670000-12679200	Weak transcription	NHLF	lung
24	chr18:12670600-12679200	Weak transcription	Fetal Heart	heart
25	chr18:12671600-12680000	Strong transcription	Fetal Intestine Large	intestine
26	chr18:12672000-12679400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr18:12672200-12701400	Weak transcription	Colonic Mucosa	Colon
28	chr18:12672400-12678400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr18:12672400-12680200	Strong transcription	HepG2	liver
30	chr18:12672400-12687400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr18:12672400-12697200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr18:12672800-12678400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr18:12673200-12701600	Weak transcription	Psoas Muscle	Psoas
34	chr18:12673400-12680200	Strong transcription	Fetal Intestine Small	intestine
35	chr18:12674200-12693800	Weak transcription	NHEK	skin
36	chr18:12674600-12678000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr18:12674600-12679400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr18:12674600-12679800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr18:12674600-12693800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr18:12674600-12701600	Weak transcription	Right Ventricle	heart
41	chr18:12674600-12701600	Weak transcription	Small Intestine	intestine
42	chr18:12674800-12678000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr18:12674800-12678000	Weak transcription	Primary B cells from cord blood	blood
44	chr18:12674800-12678000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr18:12674800-12678000	Weak transcription	Lung	lung
46	chr18:12674800-12678000	Weak transcription	Spleen	Spleen
47	chr18:12674800-12678000	Weak transcription	GM12878-XiMat	blood
48	chr18:12674800-12678200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:12674800-12679000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr18:12674800-12679000	Weak transcription	Muscle Satellite Cultured Cells	--

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