Variant report

Variant	rs4930304
Chromosome Location	chr11:65463447-65463448
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65462860..65464502-chr11:65486006..65488122,2	MCF-7	breast:
2	chr11:65461869..65464366-chr11:65623666..65626207,3	MCF-7	breast:
3	chr11:65445422..65447498-chr11:65463363..65465929,2	MCF-7	breast:
4	chr11:65429766..65432533-chr11:65462094..65464981,2	MCF-7	breast:
5	chr11:65403783..65405933-chr11:65463116..65465453,2	K562	blood:

Variant related genes	Relation type
ENSG00000172977	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000213445	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000172922	Chromatin interaction
ENSG00000172732	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10896027	0.81[CEU][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896043	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs11227248	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11227249	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11227250	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227261	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227283	0.84[ASN][1000 genomes]
rs11227284	0.81[ASN][1000 genomes]
rs11227288	0.81[ASN][1000 genomes]
rs11227302	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs1193851	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1205259	0.89[CHD][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12281400	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1784223	0.85[CHD][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1787034	0.94[CHD][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2448490	1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2509948	1.00[MEX][hapmap];0.90[TSI][hapmap]
rs3372	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs34007146	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34462081	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4930156	1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs494003	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs573589	0.85[MEX][hapmap]
rs578056	0.81[ASN][1000 genomes]
rs7395672	0.80[MEX][hapmap]
rs7944860	1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[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	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
2	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
3	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
6	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv897748	chr11:65392695-65466911	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv897755	chr11:65405300-65481166	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4930304	RNASEH2C	cis	Artery Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65459400-65466200	Enhancers	Stomach Mucosa	stomach
2	chr11:65461200-65465000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:65461600-65463800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr11:65461800-65465600	Weak transcription	K562	blood
5	chr11:65462000-65465600	Weak transcription	Esophagus	oesophagus
6	chr11:65462000-65465800	Weak transcription	Gastric	stomach
7	chr11:65462400-65468000	Enhancers	Brain Hippocampus Middle	brain
8	chr11:65462600-65464400	Enhancers	Brain Cingulate Gyrus	brain
9	chr11:65462600-65464600	Enhancers	Brain Substantia Nigra	brain
10	chr11:65462600-65467800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr11:65462800-65463800	Enhancers	Colon Smooth Muscle	Colon
12	chr11:65462800-65463800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr11:65463000-65463600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:65463000-65463600	Enhancers	Colonic Mucosa	Colon
15	chr11:65463000-65463800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr11:65463000-65463800	Enhancers	Left Ventricle	heart
17	chr11:65463000-65463800	Enhancers	Pancreas	Pancrea
18	chr11:65463000-65464000	Enhancers	Adipose Nuclei	Adipose
19	chr11:65463000-65464000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:65463000-65464000	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr11:65463000-65464000	Enhancers	HUVEC	blood vessel
22	chr11:65463000-65464200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr11:65463000-65464600	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr11:65463000-65464600	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr11:65463000-65464600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr11:65463000-65464800	Enhancers	Brain Angular Gyrus	brain
27	chr11:65463000-65465200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:65463200-65463600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:65463200-65463800	Enhancers	Fetal Muscle Leg	muscle
30	chr11:65463200-65463800	Enhancers	Fetal Stomach	stomach
31	chr11:65463200-65463800	Enhancers	HepG2	liver
32	chr11:65463200-65464000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:65463200-65464200	Enhancers	Fetal Muscle Trunk	muscle
34	chr11:65463400-65463600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:65463400-65463600	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr11:65463400-65463800	Enhancers	Brain Germinal Matrix	brain
37	chr11:65463400-65463800	Enhancers	Right Atrium	heart
38	chr11:65463400-65463800	Enhancers	HMEC	breast
39	chr11:65463400-65465000	Enhancers	Brain Anterior Caudate	brain
40	chr11:65463400-65465600	Weak transcription	Duodenum Mucosa	Duodenum

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