Variant report

Variant	rs10774871
Chromosome Location	chr12:116982722-116982723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr12:116982651-116982922	MCF10A-Er-Src	breast:	n/a	chr12:116982776-116982787 chr12:116982776-116982786
2	MYC	chr12:116982659-116982903	K562	blood:	n/a	chr12:116982776-116982787 chr12:116982776-116982786

No.	Distal block	Cell Line	Cell type
1	chr12:116970149..116972924-chr12:116980569..116984138,3	K562	blood:
2	chr12:116978005..116980165-chr12:116981045..116983272,3	K562	blood:
3	chr12:116976624..116978627-chr12:116982382..116983946,2	MCF-7	breast:
4	chr12:116967310..116968928-chr12:116982410..116984737,2	MCF-7	breast:
5	chr12:116972954..116976218-chr12:116977204..116983029,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP1LC3B2-8	chr12:116982674-116982911	NONHSAT030951

Variant related genes	Relation type
ENSG00000258102	TF binding region
ENSG00000196668	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10774872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10850662	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10850663	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068062	0.82[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068070	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068075	0.90[ASN][1000 genomes]
rs11609040	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609872	0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11610226	1.00[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];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11615960	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1394801	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1394802	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2047952	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2089222	0.94[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2102294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2893685	0.88[ASN][1000 genomes]
rs60521218	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490075	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6490076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7297552	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7300418	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7304300	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7315385	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7954181	0.93[ASN][1000 genomes]
rs7961538	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969190	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7969566	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972701	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7976256	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899540	chr12:116920503-116999861	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10774871	FLJ42957	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:116973000-116986000	Weak transcription	Aorta	Aorta
2	chr12:116975600-116984000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:116977600-116985400	Weak transcription	Placenta	Placenta
4	chr12:116977800-116984800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:116978000-116983200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:116978000-116983400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:116978000-116985800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:116978200-116985800	Weak transcription	Psoas Muscle	Psoas
9	chr12:116978200-116989400	Weak transcription	Esophagus	oesophagus
10	chr12:116978400-116983600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:116978400-116984200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:116978400-116985000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:116978400-116985800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:116978600-116983000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:116978600-116983600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:116978800-116983800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:116980000-116983800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:116980200-116984400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:116980400-116982800	Enhancers	Fetal Lung	lung
20	chr12:116980400-116983200	Enhancers	Adipose Nuclei	Adipose
21	chr12:116980400-116983800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:116980400-116983800	Enhancers	Fetal Muscle Leg	muscle
23	chr12:116980600-116984200	Enhancers	Fetal Muscle Trunk	muscle
24	chr12:116980600-116985000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:116980800-116985800	Weak transcription	Right Ventricle	heart
26	chr12:116980800-116985800	Weak transcription	NH-A	brain
27	chr12:116981000-116983000	Weak transcription	Fetal Brain Female	brain
28	chr12:116981000-116983400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:116981000-116983600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:116981000-116983600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:116981000-116985200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:116981000-116985400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:116981000-116985800	Weak transcription	Fetal Kidney	kidney
34	chr12:116981200-116985000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr12:116981200-116985400	Weak transcription	Fetal Thymus	thymus
36	chr12:116981400-116982800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr12:116981600-116984800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr12:116981600-116986000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:116981800-116983000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:116981800-116983400	Enhancers	Colon Smooth Muscle	Colon
41	chr12:116981800-116983800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:116982000-116983600	Enhancers	Ovary	ovary
43	chr12:116982000-116986000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:116982200-116982800	Enhancers	Liver	Liver
45	chr12:116982200-116983400	Enhancers	NHEK	skin
46	chr12:116982200-116984200	Enhancers	Fetal Stomach	stomach
47	chr12:116982400-116982800	Enhancers	A549	lung
48	chr12:116982400-116983400	Enhancers	HMEC	breast
49	chr12:116982400-116985200	Weak transcription	Colonic Mucosa	Colon
50	chr12:116982400-116986000	Weak transcription	Rectal Smooth Muscle	rectum

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