Variant report

Variant	rs2279500
Chromosome Location	chr1:113244433-113244434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
2	chr1:113006953..113008825-chr1:113243522..113245594,2	MCF-7	breast:
3	chr1:113160443..113165363-chr1:113242054..113245654,5	K562	blood:
4	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:
5	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
6	chr1:113239573..113244483-chr1:113252369..113259292,10	K562	blood:
7	chr1:112937481..112939065-chr1:113242426..113245199,2	MCF-7	breast:
8	chr1:113184100..113185954-chr1:113242899..113245081,2	K562	blood:
9	chr1:113193973..113196320-chr1:113243250..113245358,2	K562	blood:
10	chr1:113193696..113198407-chr1:113243250..113250056,8	K562	blood:
11	chr1:113215224..113219998-chr1:113238829..113244717,20	MCF-7	breast:
12	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
13	chr1:113134544..113137482-chr1:113243651..113245216,2	MCF-7	breast:
14	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155363	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000271810	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000238975	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000235299	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12048528	0.91[GIH][hapmap]
rs12126494	1.00[ASN][1000 genomes]
rs12138335	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12144044	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1238	0.91[GIH][hapmap]
rs12401734	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12402929	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12406906	0.91[GIH][hapmap]
rs12739994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12750621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2932529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2932534	0.91[GIH][hapmap]
rs2932537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932538	0.91[GIH][hapmap]
rs2999158	0.81[AFR][1000 genomes]
rs2999159	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3013433	1.00[ASN][1000 genomes]
rs3013441	1.00[GIH][hapmap]
rs35221527	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3790611	0.88[GIH][hapmap]
rs3790612	0.91[GIH][hapmap]
rs3795820	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6537740	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6537741	1.00[JPT][hapmap]
rs6537742	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs6537746	0.91[GIH][hapmap]
rs6658555	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6668533	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6681371	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6682678	0.84[GIH][hapmap]
rs7415988	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7535636	0.91[GIH][hapmap]
rs7551933	0.88[GIH][hapmap]
rs999923	0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
5	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2279500	DENND2C	cis	parietal	SCAN
rs2279500	FAM102B	cis	cerebellum	SCAN
rs2279500	SORT1	cis	cerebellum	SCAN
rs2279500	MOV10	cis	parietal	SCAN
rs2279500	HBXIP	cis	parietal	SCAN
rs2279500	CTTNBP2NL	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113229200-113248000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:113235800-113244600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:113238000-113246400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:113238800-113246600	Genic enhancers	Placenta Amnion	Placenta Amnion
5	chr1:113239400-113246600	Genic enhancers	Fetal Intestine Large	intestine
6	chr1:113240400-113247000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:113240400-113247200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:113240600-113244600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:113240600-113245600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:113240600-113245800	Genic enhancers	Lung	lung
11	chr1:113240600-113246800	Genic enhancers	Colonic Mucosa	Colon
12	chr1:113240600-113247000	Genic enhancers	Fetal Muscle Trunk	muscle
13	chr1:113240600-113247000	Genic enhancers	Fetal Muscle Leg	muscle
14	chr1:113240600-113247200	Genic enhancers	Placenta	Placenta
15	chr1:113240800-113244600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:113240800-113246400	Genic enhancers	Pancreas	Pancrea
17	chr1:113240800-113246600	Genic enhancers	Adipose Nuclei	Adipose
18	chr1:113240800-113247200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:113241000-113245800	Genic enhancers	Gastric	stomach
20	chr1:113241000-113246600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr1:113241200-113244600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:113241200-113244800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:113241200-113247000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
24	chr1:113241200-113247200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:113241400-113246400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:113241400-113246600	Genic enhancers	HMEC	breast
27	chr1:113241600-113247000	Genic enhancers	Fetal Intestine Small	intestine
28	chr1:113241600-113249200	Enhancers	Primary B cells from peripheral blood	blood
29	chr1:113241800-113247000	Genic enhancers	Colon Smooth Muscle	Colon
30	chr1:113242000-113248000	Enhancers	Primary B cells from cord blood	blood
31	chr1:113242200-113244600	Genic enhancers	Esophagus	oesophagus
32	chr1:113242200-113245400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:113242400-113244600	Enhancers	Small Intestine	intestine
34	chr1:113242400-113245200	Genic enhancers	Fetal Thymus	thymus
35	chr1:113242400-113246200	Genic enhancers	Left Ventricle	heart
36	chr1:113242400-113247000	Genic enhancers	Fetal Stomach	stomach
37	chr1:113242400-113247000	Genic enhancers	Spleen	Spleen
38	chr1:113242400-113247000	Genic enhancers	NHLF	lung
39	chr1:113242600-113244600	Enhancers	Ovary	ovary
40	chr1:113242600-113245400	Genic enhancers	Liver	Liver
41	chr1:113242800-113244600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr1:113242800-113244600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr1:113242800-113245800	Genic enhancers	NHDF-Ad	bronchial
44	chr1:113242800-113247000	Enhancers	Brain Substantia Nigra	brain
45	chr1:113242800-113247200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:113242800-113247800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:113243000-113245000	Enhancers	Brain Anterior Caudate	brain
48	chr1:113243000-113245400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:113243000-113245800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:113243000-113246600	Genic enhancers	Rectal Mucosa Donor 29	rectum

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