Variant report

Variant	rs279074
Chromosome Location	chr13:51102058-51102059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:20)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAL1	chr13:51101895-51102085	K562	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50698015..50701526-chr13:51100615..51103673,4	MCF-7	breast:

(count:20 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNASEH2B-3	chr13:51102002-51102200	XLOC_010390
2	lnc-RNASEH2B-3	chr13:51102002-51102200	XLOC_010390
3	lnc-RNASEH2B-3	chr13:51102002-51102200	XLOC_010390
4	lnc-RNASEH2B-3	chr13:51102002-51102200	XLOC_010390
5	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033815
6	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033816
7	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033818
8	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033821
9	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033823
10	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033828
11	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033842
12	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033850
13	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033857
14	lnc-RNASEH2B-3	chr13:51102002-51102670	NONHSAT033811
15	lnc-RNASEH2B-3	chr13:51102003-51102200	NONHSAT033847
16	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT140132
17	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033819
18	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT140131
19	lnc-RNASEH2B-3	chr13:51102002-51102200	NR_109974
20	lnc-RNASEH2B-3	chr13:51102002-51102200	NONHSAT033824

No data

Variant related genes	Relation type
ENSG00000229323	TF binding region
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1239945	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1239948	0.85[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1239951	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1239952	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs493616	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs522070	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs568043	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs644073	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7994628	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	nsv1045237	chr13:50976560-51102386	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs279074	KCNRG	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51096000-51103200	Weak transcription	Ovary	ovary
2	chr13:51096200-51102200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr13:51096600-51103400	Weak transcription	Small Intestine	intestine
4	chr13:51097200-51102800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr13:51097600-51103400	Weak transcription	Fetal Intestine Small	intestine
6	chr13:51098600-51103000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr13:51099200-51103200	Weak transcription	Liver	Liver
8	chr13:51099600-51103000	Enhancers	Dnd41	blood
9	chr13:51099800-51104000	Enhancers	Fetal Muscle Leg	muscle
10	chr13:51099800-51104000	Enhancers	Fetal Thymus	thymus
11	chr13:51099800-51104000	Enhancers	Thymus	Thymus
12	chr13:51100000-51102600	Enhancers	Primary B cells from peripheral blood	blood
13	chr13:51100000-51102800	Enhancers	Fetal Heart	heart
14	chr13:51100000-51105200	Enhancers	Primary T cells from cord blood	blood
15	chr13:51100400-51102800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:51100400-51102800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr13:51100400-51105200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr13:51100600-51102600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr13:51100600-51103200	Enhancers	Brain Hippocampus Middle	brain
20	chr13:51100600-51103400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:51100600-51103800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr13:51100600-51103800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr13:51100600-51104000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr13:51100600-51104200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr13:51100800-51102400	Enhancers	Primary T cells fromperipheralblood	blood
26	chr13:51100800-51102600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr13:51100800-51102600	Enhancers	Fetal Muscle Trunk	muscle
28	chr13:51100800-51102600	Enhancers	Placenta	Placenta
29	chr13:51100800-51102800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:51100800-51103200	Enhancers	Brain Anterior Caudate	brain
31	chr13:51100800-51103400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr13:51100800-51103400	Enhancers	Brain Cingulate Gyrus	brain
33	chr13:51100800-51103400	Enhancers	Brain Substantia Nigra	brain
34	chr13:51100800-51103800	Enhancers	Primary hematopoietic stem cells	blood
35	chr13:51100800-51104200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr13:51101000-51102200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr13:51101000-51102400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr13:51101000-51102800	Enhancers	Pancreas	Pancrea
39	chr13:51101000-51103200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr13:51101000-51103400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr13:51101000-51103400	Enhancers	Adipose Nuclei	Adipose
42	chr13:51101000-51103400	Weak transcription	Brain Germinal Matrix	brain
43	chr13:51101000-51103400	Weak transcription	Colonic Mucosa	Colon
44	chr13:51101000-51103800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr13:51101200-51102800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr13:51101200-51103000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr13:51101200-51103200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr13:51101200-51103400	Weak transcription	Fetal Lung	lung
49	chr13:51101200-51103600	Enhancers	Colon Smooth Muscle	Colon
50	chr13:51101400-51102200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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