Variant report

Variant	rs9840445
Chromosome Location	chr3:53896018-53896019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:53895860-53896668	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:53895871-53896844	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:53895880-53896361	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:53895840-53896022	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:53895751-53897353	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000271976	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1020082	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1134091	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12632292	0.98[EUR][1000 genomes]
rs17053568	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17053590	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1982171	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241806	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2276840	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276843	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276844	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276845	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2289203	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2304575	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304576	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2884631	0.90[EUR][1000 genomes]
rs3017	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733075	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3733079	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3733083	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821868	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821869	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41292476	0.92[EUR][1000 genomes]
rs4141606	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45511795	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687594	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4687753	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687756	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4687758	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4687760	0.84[EUR][1000 genomes]
rs55917919	0.89[EUR][1000 genomes]
rs56743403	0.91[EUR][1000 genomes]
rs57398949	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62253003	0.83[ASN][1000 genomes]
rs62253004	0.83[ASN][1000 genomes]
rs6445612	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6798958	0.80[YRI][hapmap]
rs709324	0.90[EUR][1000 genomes]
rs73078007	0.81[EUR][1000 genomes]
rs9849951	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9850063	0.98[EUR][1000 genomes]
rs9860367	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9880056	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs999515	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9840445	SELK	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
2	chr3:53885600-53896600	Weak transcription	Right Ventricle	heart
3	chr3:53886200-53897200	Weak transcription	Colonic Mucosa	Colon
4	chr3:53887800-53898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
6	chr3:53889000-53901400	Weak transcription	Esophagus	oesophagus
7	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:53890000-53904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:53890400-53898600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:53890400-53898800	Weak transcription	NH-A	brain
11	chr3:53890400-53903600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:53891000-53898000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:53891000-53898000	Weak transcription	Spleen	Spleen
15	chr3:53891000-53914200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:53891000-53914200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:53891200-53897800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:53891200-53898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:53891200-53900800	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:53891200-53910800	Strong transcription	Fetal Stomach	stomach
21	chr3:53891400-53898400	Weak transcription	Small Intestine	intestine
22	chr3:53891400-53914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:53891600-53897800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:53891600-53904000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:53891800-53912800	Strong transcription	Brain Germinal Matrix	brain
26	chr3:53892000-53914400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:53892200-53897000	Strong transcription	Fetal Intestine Large	intestine
28	chr3:53892200-53912400	Strong transcription	Fetal Brain Female	brain
29	chr3:53892200-53914000	Strong transcription	Adipose Nuclei	Adipose
30	chr3:53892200-53914400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:53892200-53914600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:53892400-53899400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr3:53892400-53904800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:53892400-53906200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:53892400-53913000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:53892400-53913800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:53892400-53914200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr3:53892400-53914400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:53892600-53896400	Weak transcription	HUVEC	blood vessel
40	chr3:53892600-53914200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:53892600-53914400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:53892600-53914400	Strong transcription	Fetal Muscle Leg	muscle
43	chr3:53892800-53914200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:53892800-53914200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr3:53892800-53914200	Strong transcription	Thymus	Thymus
46	chr3:53892800-53914400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:53892800-53914600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:53893000-53896400	Strong transcription	GM12878-XiMat	blood
49	chr3:53893000-53914000	Strong transcription	Placenta	Placenta
50	chr3:53893000-53914400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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