Variant report

Variant	rs9429495
Chromosome Location	chr1:113412089-113412090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113393846..113396397-chr1:113410611..113412289,2	K562	blood:
2	chr1:113411911..113414258-chr1:113419696..113422107,2	MCF-7	breast:
3	chr1:113405858..113408757-chr1:113410736..113413457,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11102557	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11102558	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11576349	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12068893	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1216537	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs1237670	0.88[CEU][hapmap]
rs2996294	0.85[CEU][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes]
rs2996389	0.85[CEU][hapmap]
rs7546994	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9429496	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv818378	chr1:113263711-113434818	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1008434	chr1:113288282-113447426	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	esv3374684	chr1:113359959-113414316	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	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
15	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
16	esv3360645	chr1:113375959-113414652	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv3362439	chr1:113376621-113450321	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9429495	LRIG2	cis	cerebellum	SCAN
rs9429495	DENND2C	cis	parietal	SCAN
rs9429495	AKNAD1	cis	cerebellum	SCAN
rs9429495	SLC16A1	Cis_1M	lymphoblastoid	RTeQTL
rs9429495	ATP1A1	cis	cerebellum	SCAN
rs9429495	OVGP1	cis	cerebellum	SCAN
rs9429495	DENND2C	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113405800-113418200	Enhancers	Placenta	Placenta
2	chr1:113408000-113413800	Enhancers	HUVEC	blood vessel
3	chr1:113408600-113412200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:113408600-113412400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:113408600-113412400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:113408600-113412400	Enhancers	HMEC	breast
7	chr1:113409200-113415000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:113409400-113412200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:113409400-113412400	Enhancers	NHEK	skin
10	chr1:113409800-113413400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:113409800-113415000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:113409800-113415000	Weak transcription	Osteobl	bone
13	chr1:113411200-113412400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:113411200-113414000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:113411200-113415400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:113411200-113415400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:113411400-113413000	Enhancers	K562	blood
18	chr1:113411400-113414200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:113411600-113412200	Enhancers	Fetal Intestine Large	intestine
20	chr1:113411600-113412400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:113411600-113413000	Enhancers	Stomach Mucosa	stomach
22	chr1:113411600-113416000	Enhancers	Fetal Intestine Small	intestine
23	chr1:113411800-113412200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr1:113411800-113412200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:113411800-113412400	Enhancers	Hela-S3	cervix
26	chr1:113411800-113413200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:113411800-113415200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:113412000-113412200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:113412000-113413200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:113412000-113413400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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