Variant report

Variant	rs2999155
Chromosome Location	chr1:113221658-113221659
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113160823..113162360-chr1:113220552..113222913,2	K562	blood:
2	chr1:113158395..113164969-chr1:113214433..113222934,24	MCF-7	breast:
3	chr1:113192182..113194200-chr1:113220715..113222774,2	K562	blood:
4	chr1:113216623..113219353-chr1:113219400..113223773,8	MCF-7	breast:
5	chr1:113220341..113222791-chr1:113241628..113243660,3	MCF-7	breast:
6	chr1:113217617..113223835-chr1:113226384..113230990,8	MCF-7	breast:
7	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
8	chr1:113214590..113222957-chr1:113244863..113253590,39	MCF-7	breast:
9	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:

No data

Variant related genes	Relation type
ENSG00000155366	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000225075	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000271810	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10745330	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs10776755	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs10776757	0.89[CEU][hapmap]
rs10857963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs11102512	0.85[AMR][1000 genomes]
rs11584092	0.88[CEU][hapmap]
rs12046208	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs12046329	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12046466	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12126277	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs12728001	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1994604	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932532	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932536	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999154	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2999157	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3013431	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3013439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3013440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3103450	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351372	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs4838959	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs4839254	0.85[CEU][hapmap]
rs6537748	0.87[TSI][hapmap]
rs6537749	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs6666579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs6669096	0.85[AMR][1000 genomes]
rs6682737	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes]
rs6691932	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6700673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7415820	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7513716	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs7522288	0.82[CEU][hapmap]
rs7524494	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7544663	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap]
rs7546094	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7554345	0.87[AMR][1000 genomes]
rs7554916	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs902289	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs910697	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs9429486	0.89[CEU][hapmap]
rs954679	0.95[JPT][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	esv13773	chr1:113220144-113225122	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2999155	ST7L	cis	lymphoblastoid	seeQTL
rs2999155	ST7L	cis	multi-tissue	Pritchard
rs2999155	ST7L	cis	Heart Left Ventricle	GTEx
rs2999155	ST7L	cis	lung	GTEx
rs2999155	ST7L	cis	Adipose Subcutaneous	GTEx
rs2999155	ST7L	cis	Esophagus Muscularis	GTEx
rs2999155	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs2999155	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs2999155	SYCP1	cis	parietal	SCAN
rs2999155	ST7L	cis	Thyroid	GTEx
rs2999155	ST7L	cis	Nerve Tibial	GTEx
rs2999155	C1orf162	cis	parietal	SCAN
rs2999155	WNT2B	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113218400-113230200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:113218400-113230400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:113218400-113234200	Weak transcription	Aorta	Aorta
4	chr1:113218600-113230200	Weak transcription	Lung	lung
5	chr1:113218600-113232200	Weak transcription	Ovary	ovary
6	chr1:113218600-113235000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:113218600-113235400	Weak transcription	HSMM	muscle
8	chr1:113218600-113240800	Weak transcription	Right Atrium	heart
9	chr1:113218800-113222200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:113218800-113222800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:113218800-113229200	Weak transcription	Placenta	Placenta
12	chr1:113218800-113230000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:113218800-113230000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:113218800-113230200	Weak transcription	Left Ventricle	heart
15	chr1:113218800-113230400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:113218800-113230600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:113218800-113232200	Weak transcription	Colonic Mucosa	Colon
18	chr1:113218800-113232400	Weak transcription	Brain Substantia Nigra	brain
19	chr1:113218800-113234200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:113219000-113222000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:113219000-113223400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:113219000-113228600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:113219000-113228800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:113219000-113228800	Weak transcription	Osteobl	bone
25	chr1:113219000-113230200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:113219000-113230600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:113219000-113231400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:113219000-113232000	Weak transcription	Hela-S3	cervix
29	chr1:113219000-113232200	Weak transcription	Small Intestine	intestine
30	chr1:113219000-113232400	Weak transcription	Brain Anterior Caudate	brain
31	chr1:113219000-113234400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:113219000-113235400	Weak transcription	A549	lung
33	chr1:113219000-113242200	Weak transcription	NHDF-Ad	bronchial
34	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
35	chr1:113219200-113224000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:113219200-113228600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:113219200-113228600	Weak transcription	NHEK	skin
38	chr1:113219200-113228800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:113219200-113228800	Weak transcription	HMEC	breast
40	chr1:113219200-113230800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:113219200-113230800	Weak transcription	NHLF	lung
42	chr1:113219200-113232200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:113219200-113232400	Weak transcription	HUVEC	blood vessel
44	chr1:113219400-113228600	Weak transcription	Liver	Liver
45	chr1:113219400-113229000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:113219400-113230200	Weak transcription	Primary T cells from cord blood	blood
47	chr1:113219400-113230200	Weak transcription	Adipose Nuclei	Adipose
48	chr1:113219400-113230400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:113219400-113230400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:113219400-113230600	Weak transcription	Rectal Mucosa Donor 29	rectum

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