Variant report

Variant	rs773433
Chromosome Location	chr1:113541801-113541802
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:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113541670..113543252-chr9:124968243..124969763,2	MCF-7	breast:
2	chr1:113493684..113495226-chr1:113539915..113542867,2	K562	blood:
3	chr1:113540112..113542991-chr1:113560118..113562958,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRIG2-4	chr1:113541552-113542118	ENSG00000226419
2	lnc-SLC16A1-4	chr1:113541027-113542835	ucscGeneNc_uc001edg_1
3	lnc-LRIG2-3	chr1:113541552-113542118	ENSG00000226419.2
4	lnc-LRIG2-3	chr1:113541768-113541804	NONHSAT005308

No data

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1049434	0.88[CEU][hapmap];0.93[GIH][hapmap];0.82[EUR][1000 genomes]
rs10857980	0.83[CEU][hapmap];0.86[GIH][hapmap]
rs11102573	0.87[ASN][1000 genomes]
rs11102574	0.88[ASN][1000 genomes]
rs11102575	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11102576	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11102582	0.81[JPT][hapmap]
rs11584099	0.86[ASN][1000 genomes]
rs11584535	0.88[ASN][1000 genomes]
rs11588345	0.87[ASN][1000 genomes]
rs11590170	0.88[ASN][1000 genomes]
rs11590174	0.88[ASN][1000 genomes]
rs12128904	0.86[ASN][1000 genomes]
rs12129863	0.87[ASN][1000 genomes]
rs1216603	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1216772	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1216773	0.87[ASN][1000 genomes]
rs1216775	0.87[ASN][1000 genomes]
rs1216779	0.88[ASN][1000 genomes]
rs1216781	0.89[JPT][hapmap]
rs1216783	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1216784	0.84[ASN][1000 genomes]
rs1216785	0.86[ASN][1000 genomes]
rs12184285	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12354228	0.87[ASN][1000 genomes]
rs12744009	0.83[JPT][hapmap]
rs12745675	0.88[ASN][1000 genomes]
rs12746771	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1539624	0.84[CEU][hapmap]
rs1544227	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1627925	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1629027	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs17014850	0.87[ASN][1000 genomes]
rs17030901	0.87[ASN][1000 genomes]
rs17030905	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs17030974	0.89[JPT][hapmap]
rs1728218	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1728219	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1728232	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1728238	0.83[JPT][hapmap]
rs1766862	0.88[JPT][hapmap]
rs1778024	0.89[JPT][hapmap]
rs1778025	0.89[JPT][hapmap]
rs1983929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2769259	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2798691	0.87[ASN][1000 genomes]
rs2798692	0.87[ASN][1000 genomes]
rs34233065	0.87[ASN][1000 genomes]
rs34565381	0.89[ASN][1000 genomes]
rs3789592	0.88[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs3889656	0.87[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs61818171	0.87[ASN][1000 genomes]
rs61818172	0.87[ASN][1000 genomes]
rs61818173	0.87[ASN][1000 genomes]
rs61818174	0.87[ASN][1000 genomes]
rs61818176	0.81[ASN][1000 genomes]
rs6537764	0.84[EUR][1000 genomes]
rs6537765	0.92[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs6656041	0.87[ASN][1000 genomes]
rs6656311	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs6663872	0.83[EUR][1000 genomes]
rs6681037	0.81[CEU][hapmap]
rs71659385	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7169	0.88[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs7551223	0.81[EUR][1000 genomes]
rs7556664	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs773430	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773432	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773434	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs773435	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs773436	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs773439	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs773440	0.94[ASN][1000 genomes]
rs773442	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9633370	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs9787311	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs773433	OVGP1	cis	cerebellum	SCAN
rs773433	DENND2C	cis	parietal	SCAN
rs773433	SLC6A17	cis	parietal	SCAN
rs773433	AMPD1	cis	parietal	SCAN
rs773433	LRIG2	cis	cerebellum	SCAN
rs773433	OLFML3	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113511200-113545800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:113511200-113546400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr1:113511200-113558000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:113511200-113558600	Weak transcription	NHDF-Ad	bronchial
5	chr1:113511200-113564000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:113517800-113542800	Weak transcription	Dnd41	blood
7	chr1:113526600-113564200	Weak transcription	Placenta	Placenta
8	chr1:113526800-113558600	Weak transcription	GM12878-XiMat	blood
9	chr1:113528200-113556600	Weak transcription	Small Intestine	intestine
10	chr1:113529000-113554400	Weak transcription	Lung	lung
11	chr1:113533600-113555600	Weak transcription	Fetal Lung	lung
12	chr1:113534400-113548400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:113535400-113544200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:113535600-113543400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr1:113535600-113549200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:113535600-113552200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:113535600-113557000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:113535800-113550600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:113535800-113564000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:113535800-113564000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:113535800-113564200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:113535800-113568800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:113537000-113543000	Enhancers	Fetal Heart	heart
24	chr1:113537200-113554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:113537400-113546000	Weak transcription	NHLF	lung
26	chr1:113537400-113550400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:113537400-113554200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:113537600-113552800	Weak transcription	Fetal Thymus	thymus
29	chr1:113538400-113545200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:113538600-113542800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:113538600-113558600	Weak transcription	Spleen	Spleen
32	chr1:113538800-113546000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:113539200-113547000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:113539600-113564200	Weak transcription	Brain Germinal Matrix	brain
35	chr1:113539800-113543200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:113540000-113542200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:113540000-113542400	Enhancers	Rectal Smooth Muscle	rectum
38	chr1:113540000-113542800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr1:113540000-113542800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:113540000-113542800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:113540000-113543200	Enhancers	Colon Smooth Muscle	Colon
42	chr1:113540200-113542000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:113540200-113542000	Genic enhancers	Adipose Nuclei	Adipose
44	chr1:113540200-113542000	Enhancers	Brain Anterior Caudate	brain
45	chr1:113540200-113542000	Enhancers	Brain Hippocampus Middle	brain
46	chr1:113540200-113542000	Enhancers	Brain Substantia Nigra	brain
47	chr1:113540200-113542000	Enhancers	Fetal Intestine Large	intestine
48	chr1:113540200-113542000	Enhancers	HSMMtube	muscle
49	chr1:113540200-113542200	Enhancers	Brain Angular Gyrus	brain
50	chr1:113540200-113542200	Genic enhancers	Fetal Muscle Leg	muscle

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