Variant report

Variant	rs11057276
Chromosome Location	chr12:123820397-123820398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123808230..123810207-chr12:123820394..123822529,2	K562	blood:
2	chr12:123820310..123822870-chr12:123823085..123825234,2	MCF-7	breast:
3	chr12:123819626..123821954-chr12:123832677..123835923,3	K562	blood:

Variant related genes	Relation type
ENSG00000139697	Chromatin interaction
ENSG00000207189	Chromatin interaction

Extended variants
information (count: 184 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs10082867	1.00[ASN][1000 genomes]
rs10444439	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10444449	0.85[ASN][1000 genomes]
rs1051434	0.82[TSI][hapmap]
rs10744151	0.80[JPT][hapmap]
rs10744152	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs10744153	0.83[ASN][1000 genomes]
rs10744154	0.83[ASN][1000 genomes]
rs10772997	0.84[JPT][hapmap]
rs10773000	0.97[GIH][hapmap];0.94[JPT][hapmap]
rs10773002	0.83[ASW][hapmap]
rs10773003	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10773004	0.98[ASN][1000 genomes]
rs10773005	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10773006	0.98[ASN][1000 genomes]
rs10773018	0.82[ASN][1000 genomes]
rs10846489	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap]
rs10846497	0.84[ASN][1000 genomes]
rs10846505	0.91[ASN][1000 genomes]
rs10846506	0.97[ASN][1000 genomes]
rs10846517	0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs10846519	0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs10846523	0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs11057223	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs11057238	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11057242	0.94[ASN][1000 genomes]
rs11057248	0.95[ASN][1000 genomes]
rs11057251	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057254	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057261	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057273	0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs11057275	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057283	0.83[ASN][1000 genomes]
rs11057284	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057287	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1109559	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap]
rs1109560	0.94[JPT][hapmap]
rs11503021	0.96[ASN][1000 genomes]
rs11608297	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11608305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11611141	1.00[ASN][1000 genomes]
rs11611677	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11611679	0.95[ASN][1000 genomes]
rs11611680	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11611694	1.00[ASN][1000 genomes]
rs11612234	0.83[ASN][1000 genomes]
rs12317103	1.00[ASN][1000 genomes]
rs12317452	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12366872	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12367421	0.97[ASN][1000 genomes]
rs12582153	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13303208	0.93[ASN][1000 genomes]
rs1568427	0.83[ASW][hapmap]
rs1568428	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap]
rs1615350	0.83[ASW][hapmap];0.84[JPT][hapmap]
rs1727293	1.00[ASW][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs1727301	0.85[JPT][hapmap]
rs1727302	0.84[JPT][hapmap]
rs1790104	0.85[JPT][hapmap]
rs1879379	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap]
rs2271976	0.94[JPT][hapmap]
rs2277343	0.82[AMR][1000 genomes]
rs2682427	0.85[JPT][hapmap]
rs28410096	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28414347	0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs28417583	0.81[ASN][1000 genomes]
rs28418709	0.83[ASN][1000 genomes]
rs28419092	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450974	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28461471	0.98[ASN][1000 genomes]
rs28496545	0.92[ASN][1000 genomes]
rs28498205	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28501453	0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs28503862	0.98[ASN][1000 genomes]
rs28516750	0.94[ASN][1000 genomes]
rs28517382	0.83[ASN][1000 genomes]
rs28532037	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28533432	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28537583	0.81[ASN][1000 genomes]
rs28546238	0.81[ASN][1000 genomes]
rs28556815	0.88[ASN][1000 genomes]
rs28565984	0.85[ASN][1000 genomes]
rs28574664	0.83[ASN][1000 genomes]
rs28577594	0.93[ASN][1000 genomes]
rs28581850	0.98[ASN][1000 genomes]
rs28587386	0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs28592032	0.98[ASN][1000 genomes]
rs28594416	0.83[ASN][1000 genomes]
rs28595660	0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs28602967	0.81[ASN][1000 genomes]
rs28611282	0.81[ASN][1000 genomes]
rs28613486	0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs28627651	0.81[ASN][1000 genomes]
rs28631104	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28631903	0.83[ASN][1000 genomes]
rs28642812	0.93[ASN][1000 genomes]
rs28660993	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs28681105	0.81[ASN][1000 genomes]
rs28690326	0.86[ASN][1000 genomes]
rs28703745	0.82[ASN][1000 genomes]
rs28718696	0.82[ASN][1000 genomes]
rs28759130	0.83[ASN][1000 genomes]
rs28786830	0.98[ASN][1000 genomes]
rs28820735	0.98[ASN][1000 genomes]
rs28825193	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28865692	0.80[ASN][1000 genomes]
rs28866344	0.94[ASN][1000 genomes]
rs28885203	0.80[ASN][1000 genomes]
rs3088303	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34032470	0.88[ASN][1000 genomes]
rs35818434	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803001	0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3825141	0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4759374	0.81[ASN][1000 genomes]
rs4759375	0.98[ASN][1000 genomes]
rs4759376	0.83[ASN][1000 genomes]
rs4759377	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4759421	0.83[ASN][1000 genomes]
rs56116847	0.99[ASN][1000 genomes]
rs56197170	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56309603	0.90[ASN][1000 genomes]
rs57356592	0.81[ASN][1000 genomes]
rs57416942	0.83[ASN][1000 genomes]
rs58537268	0.81[ASN][1000 genomes]
rs58948739	0.81[ASN][1000 genomes]
rs59295450	0.83[ASN][1000 genomes]
rs60755632	0.81[ASN][1000 genomes]
rs60835840	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61058270	0.81[ASN][1000 genomes]
rs61388686	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61751327	0.83[ASN][1000 genomes]
rs61955125	0.90[ASN][1000 genomes]
rs6416290	0.87[ASN][1000 genomes]
rs6488868	0.84[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs6488869	0.83[ASN][1000 genomes]
rs6488870	0.83[ASN][1000 genomes]
rs6488871	0.83[ASN][1000 genomes]
rs6488872	0.83[ASN][1000 genomes]
rs6488873	0.91[ASN][1000 genomes]
rs7137243	0.83[ASN][1000 genomes]
rs7139321	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs7297649	0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs7298909	1.00[ASN][1000 genomes]
rs7301163	0.83[ASN][1000 genomes]
rs7303754	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7304782	0.83[ASW][hapmap]
rs7310756	0.83[ASN][1000 genomes]
rs7311304	0.83[ASN][1000 genomes]
rs7312145	1.00[ASN][1000 genomes]
rs7315453	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73216931	0.93[ASN][1000 genomes]
rs73231950	0.97[ASN][1000 genomes]
rs7484644	0.83[ASN][1000 genomes]
rs7485967	0.83[ASN][1000 genomes]
rs7486223	0.83[ASN][1000 genomes]
rs7488340	0.83[ASN][1000 genomes]
rs7488490	0.82[ASN][1000 genomes]
rs7952835	0.83[ASN][1000 genomes]
rs7954704	1.00[ASN][1000 genomes]
rs7955367	0.83[ASN][1000 genomes]
rs7959415	0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7970080	0.83[ASN][1000 genomes]
rs7972811	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7973131	0.83[ASN][1000 genomes]
rs7973878	0.83[ASN][1000 genomes]
rs7974099	0.88[ASN][1000 genomes]
rs7977563	0.83[ASN][1000 genomes]
rs9284166	0.83[ASN][1000 genomes]
rs9300257	0.83[ASN][1000 genomes]
rs9300259	0.82[ASN][1000 genomes]
rs9669169	0.83[ASN][1000 genomes]
rs9669273	1.00[ASN][1000 genomes]
rs9669295	0.99[ASN][1000 genomes]
rs9705407	0.96[ASN][1000 genomes]
rs9739171	1.00[ASN][1000 genomes]
rs9739565	0.83[ASN][1000 genomes]
rs9795593	0.94[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS 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 miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers 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	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers 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	70 gene(s)	inside rSNPs	diseases
5	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11057276	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs11057276	PITPNM2	cis	cerebellum	SCAN
rs11057276	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs11057276	SETD8	Cis_1M	lymphoblastoid	RTeQTL
rs11057276	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs11057276	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs11057276	TMEM120B	cis	parietal	SCAN
rs11057276	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs11057276	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs11057276	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123772400-123847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:123772800-123821000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:123773000-123835200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:123773200-123830600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:123773200-123834200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:123773200-123835000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:123773200-123835000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:123773200-123838000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:123773400-123826200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:123773400-123826200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:123773400-123826600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:123773400-123835000	Strong transcription	Fetal Thymus	thymus
13	chr12:123773400-123835400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:123773400-123837200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:123773600-123830800	Strong transcription	Placenta	Placenta
16	chr12:123773600-123835200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:123773600-123835400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:123773800-123826200	Strong transcription	Adipose Nuclei	Adipose
19	chr12:123773800-123826200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr12:123773800-123834800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr12:123773800-123837200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:123773800-123837400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:123774000-123820600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:123774000-123821600	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:123774000-123835000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr12:123774000-123835200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:123774000-123835400	Strong transcription	Dnd41	blood
28	chr12:123774400-123821200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:123774600-123822200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr12:123775600-123835400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:123775800-123821000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:123776200-123826000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr12:123776200-123830600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr12:123776400-123835000	Strong transcription	Thymus	Thymus
35	chr12:123776600-123834400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:123777000-123835400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:123777600-123834800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:123778800-123822600	Strong transcription	Liver	Liver
39	chr12:123780000-123830600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:123785600-123826200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr12:123785600-123830800	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:123785600-123835000	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:123786000-123825800	Strong transcription	Fetal Lung	lung
44	chr12:123790200-123835000	Strong transcription	Fetal Intestine Large	intestine
45	chr12:123799400-123826000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:123799600-123822200	Strong transcription	HUVEC	blood vessel
47	chr12:123799800-123833000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr12:123805000-123834000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr12:123805200-123835200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:123807600-123845200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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