Variant report

Variant	rs11168371
Chromosome Location	chr12:48437686-48437687
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48416842..48418454-chr12:48435864..48437741,2	MCF-7	breast:
2	chr12:48428906..48431676-chr12:48435313..48438563,3	MCF-7	breast:
3	chr12:48435313..48437988-chr12:48451982..48454529,2	K562	blood:
4	chr12:48433439..48436867-chr12:48436934..48440362,3	K562	blood:
5	chr12:48383628..48385806-chr12:48436712..48438837,2	K562	blood:

Extended variants
information (count: 106 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10082861	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10219623	1.00[JPT][hapmap]
rs10467101	0.84[JPT][hapmap]
rs10875720	0.91[ASN][1000 genomes]
rs10875722	0.91[ASN][1000 genomes]
rs10875723	0.92[ASN][1000 genomes]
rs10875724	0.84[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs10875725	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs10875728	0.92[EUR][1000 genomes]
rs10875729	0.92[EUR][1000 genomes]
rs10875730	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875731	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875735	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs10875738	0.81[EUR][1000 genomes]
rs10875740	0.81[EUR][1000 genomes]
rs10875745	0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap]
rs10875746	0.82[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs10875747	0.81[EUR][1000 genomes]
rs10875748	0.81[EUR][1000 genomes]
rs10875750	0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs10875767	0.93[JPT][hapmap]
rs10875770	0.93[JPT][hapmap]
rs10875772	0.93[JPT][hapmap];0.82[MEX][hapmap]
rs11168355	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs11168357	0.95[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.92[ASN][1000 genomes]
rs11168369	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168370	0.95[EUR][1000 genomes]
rs11168374	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168383	0.83[ASN][1000 genomes]
rs11168386	0.83[ASN][1000 genomes]
rs11168401	0.81[EUR][1000 genomes]
rs11168403	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11168413	1.00[JPT][hapmap]
rs11168414	0.93[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs11168418	0.93[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs11168420	0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs11168421	0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs11168425	0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs11168427	0.93[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs11168433	0.93[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs11168450	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs11168459	0.93[JPT][hapmap]
rs12296244	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297004	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12297470	0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs12301339	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12304476	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs12305182	0.83[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12305511	0.87[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs12306451	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs12310813	0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs12310999	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311774	0.83[ASN][1000 genomes]
rs12311953	0.83[ASN][1000 genomes]
rs12312134	0.93[JPT][hapmap]
rs12313300	0.83[ASN][1000 genomes]
rs12313404	0.81[EUR][1000 genomes]
rs17122620	0.83[ASN][1000 genomes]
rs17122666	0.93[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap]
rs17122812	0.93[JPT][hapmap]
rs1859445	0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2012773	1.00[JPT][hapmap]
rs2079295	0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2107638	1.00[JPT][hapmap]
rs2158516	0.81[EUR][1000 genomes]
rs2228500	0.93[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2269933	0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs2269935	0.93[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs2269936	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286021	0.81[EUR][1000 genomes]
rs28459711	0.91[ASN][1000 genomes]
rs3782910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3782911	0.81[EUR][1000 genomes]
rs4760609	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs4760610	0.94[ASN][1000 genomes]
rs4760619	1.00[JPT][hapmap]
rs4760622	0.87[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs4760676	0.96[ASN][1000 genomes]
rs4760680	0.83[ASN][1000 genomes]
rs4760681	0.93[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs4760687	0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4760695	0.87[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs4760696	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4760697	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs58952582	0.83[ASN][1000 genomes]
rs60761335	0.83[ASN][1000 genomes]
rs61918774	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918806	0.81[EUR][1000 genomes]
rs61918810	0.81[EUR][1000 genomes]
rs6580659	1.00[JPT][hapmap]
rs7135779	1.00[JPT][hapmap]
rs719008	0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs725454	0.93[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs7299135	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs7299271	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs7299364	0.91[ASN][1000 genomes]
rs73102065	0.81[EUR][1000 genomes]
rs7486424	1.00[JPT][hapmap]
rs7964359	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs8804	0.93[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs886588	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs989144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11168371	H1FNT	cis	cerebellum	SCAN
rs11168371	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs11168371	IRAK4	cis	parietal	SCAN
rs11168371	RP1-228P16.1	cis	Artery Tibial	GTEx
rs11168371	RP1-228P16.1	cis	Thyroid	GTEx
rs11168371	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs11168371	LOC255411	cis	cerebellum	SCAN
rs11168371	SENP1	cis	cerebellum	SCAN
rs11168371	ASB8	cis	cerebellum	SCAN
rs11168371	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11168371	PRKAG1	cis	parietal	SCAN
rs11168371	SENP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48422800-48438800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:48431400-48438200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:48431400-48438400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:48431600-48437800	Weak transcription	Brain Germinal Matrix	brain
5	chr12:48431800-48438200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:48431800-48438200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:48431800-48438200	Weak transcription	Fetal Stomach	stomach
8	chr12:48431800-48438200	Weak transcription	Lung	lung
9	chr12:48431800-48438200	Weak transcription	Pancreas	Pancrea
10	chr12:48431800-48438400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:48431800-48438400	Weak transcription	K562	blood
12	chr12:48431800-48438800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:48431800-48456600	Weak transcription	NHLF	lung
14	chr12:48432000-48438200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:48432000-48438200	Weak transcription	Right Ventricle	heart
16	chr12:48432000-48438200	Weak transcription	Spleen	Spleen
17	chr12:48432000-48438400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:48432000-48438400	Weak transcription	Fetal Kidney	kidney
19	chr12:48432000-48438400	Weak transcription	Ovary	ovary
20	chr12:48432000-48438800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr12:48432000-48438800	Weak transcription	NHDF-Ad	bronchial
22	chr12:48432000-48439800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:48432000-48439800	Weak transcription	Fetal Heart	heart
24	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:48432200-48438200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:48432200-48438200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:48432200-48438400	Weak transcription	HepG2	liver
28	chr12:48432200-48438400	Weak transcription	HSMMtube	muscle
29	chr12:48432200-48438600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:48432400-48438200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:48433000-48438200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:48433200-48438200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:48433200-48438600	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:48433400-48438200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:48433400-48438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:48433800-48438200	Weak transcription	Fetal Brain Female	brain
38	chr12:48433800-48438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:48434000-48437800	Weak transcription	Thymus	Thymus
40	chr12:48434000-48438200	Weak transcription	Colonic Mucosa	Colon
41	chr12:48434000-48438200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:48434000-48438200	Weak transcription	Small Intestine	intestine
43	chr12:48434400-48438200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:48434400-48439200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:48434600-48437800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:48434600-48438200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:48434800-48438200	Weak transcription	Left Ventricle	heart
48	chr12:48434800-48438400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:48434800-48438400	Weak transcription	Brain Substantia Nigra	brain
50	chr12:48434800-48438400	Weak transcription	Esophagus	oesophagus

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