Variant report

Variant	rs11169718
Chromosome Location	chr12:51533176-51533177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51477465..51479681-chr12:51531530..51534326,2	K562	blood:
2	chr12:51475866..51477468-chr12:51532284..51535126,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10783412	1.00[JPT][hapmap]
rs11169717	1.00[CEU][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169719	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169724	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12369066	1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12372440	1.00[ASN][1000 genomes]
rs12423207	1.00[JPT][hapmap]
rs150909	1.00[JPT][hapmap]
rs161044	1.00[JPT][hapmap]
rs161045	1.00[JPT][hapmap]
rs161046	1.00[JPT][hapmap]
rs161047	1.00[JPT][hapmap]
rs17125367	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17125370	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17125416	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125418	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125428	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17229232	1.00[JPT][hapmap]
rs224566	1.00[JPT][hapmap]
rs224569	1.00[JPT][hapmap]
rs224570	1.00[JPT][hapmap]
rs224573	1.00[JPT][hapmap]
rs224574	1.00[JPT][hapmap]
rs2630362	1.00[JPT][hapmap]
rs364627	1.00[JPT][hapmap]
rs445520	1.00[JPT][hapmap]
rs4768959	1.00[JPT][hapmap]
rs4768973	1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs59372312	1.00[ASN][1000 genomes]
rs6580779	1.00[JPT][hapmap]
rs6580783	1.00[JPT][hapmap]
rs73305715	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305721	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305734	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960097	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971712	1.00[JPT][hapmap]
rs7972608	1.00[JPT][hapmap]
rs7974923	1.00[JPT][hapmap]
rs7975628	1.00[JPT][hapmap]

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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	esv2762980	chr12:51527963-51561056	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11169718	METTL7A	cis	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:51503200-51560200	Weak transcription	Right Ventricle	heart
3	chr12:51504800-51563400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:51507800-51539800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:51508000-51543000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:51510200-51536200	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:51510200-51554400	Weak transcription	K562	blood
8	chr12:51511400-51558800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:51512800-51535600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:51513000-51565400	Weak transcription	Fetal Lung	lung
11	chr12:51517200-51547600	Weak transcription	Fetal Kidney	kidney
12	chr12:51517200-51554600	Weak transcription	HepG2	liver
13	chr12:51519000-51533800	Weak transcription	Gastric	stomach
14	chr12:51519000-51541000	Weak transcription	Brain Substantia Nigra	brain
15	chr12:51519000-51561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:51519000-51565000	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:51519000-51565200	Weak transcription	Left Ventricle	heart
18	chr12:51519000-51565200	Weak transcription	Pancreas	Pancrea
19	chr12:51519000-51565800	Weak transcription	Esophagus	oesophagus
20	chr12:51519200-51533800	Weak transcription	Spleen	Spleen
21	chr12:51519200-51534000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:51519200-51535400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:51519200-51537800	Weak transcription	Liver	Liver
24	chr12:51519200-51540000	Weak transcription	Thymus	Thymus
25	chr12:51519200-51542000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:51519200-51544400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:51519200-51544600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:51519200-51554600	Weak transcription	NHDF-Ad	bronchial
29	chr12:51519200-51559600	Weak transcription	Lung	lung
30	chr12:51519200-51563800	Weak transcription	Fetal Brain Female	brain
31	chr12:51519200-51565000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:51519400-51550200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:51519400-51565200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:51521200-51535800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:51521400-51533600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:51521400-51534600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:51521600-51541800	Weak transcription	NHLF	lung
38	chr12:51521600-51565200	Weak transcription	HSMM	muscle
39	chr12:51521800-51538400	Weak transcription	HMEC	breast
40	chr12:51523000-51535600	Weak transcription	NH-A	brain
41	chr12:51523200-51535600	Weak transcription	Brain Germinal Matrix	brain
42	chr12:51523400-51533400	Weak transcription	Osteobl	bone
43	chr12:51523600-51544400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:51526000-51558800	Weak transcription	GM12878-XiMat	blood
45	chr12:51526400-51538600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr12:51526800-51542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:51526800-51556400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:51527200-51541000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:51527200-51542200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr12:51527400-51565200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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