Variant report

Variant	rs2029318
Chromosome Location	chr3:112125477-112125478
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1386897	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586508	1.00[ASN][1000 genomes]
rs1872986	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1872987	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996724	1.00[ASN][1000 genomes]
rs2087259	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129856	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244035	1.00[ASN][1000 genomes]
rs2263365	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633541	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633554	1.00[ASN][1000 genomes]
rs2633567	1.00[ASN][1000 genomes]
rs2633570	1.00[ASN][1000 genomes]
rs2633576	0.80[EUR][1000 genomes]
rs2633591	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633595	1.00[ASN][1000 genomes]
rs2633601	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633606	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633607	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633608	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683890	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683896	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683897	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683898	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683901	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683902	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683903	0.97[EUR][1000 genomes]
rs2683904	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2931761	1.00[ASN][1000 genomes]
rs2971206	1.00[ASN][1000 genomes]
rs6799765	1.00[ASN][1000 genomes]
rs72952469	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877341	chr3:112079277-112125521	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1002567	chr3:112088498-112144063	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2830128	chr3:112090292-112144026	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv997659	chr3:112099148-112135687	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112115200-112127600	Weak transcription	Fetal Kidney	kidney
2	chr3:112116400-112126800	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr3:112117000-112125600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:112118600-112130400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:112120800-112126600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:112122000-112125800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:112122000-112126600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:112122400-112126000	Weak transcription	Fetal Intestine Large	intestine
9	chr3:112122400-112126200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:112122600-112125800	Weak transcription	Fetal Intestine Small	intestine
11	chr3:112123600-112125600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:112123600-112126800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr3:112123800-112128800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:112124000-112126200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr3:112124400-112126200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:112124400-112127000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr3:112124800-112126400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:112124800-112127000	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:112124800-112127400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:112125000-112126000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:112125000-112126200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:112125200-112125800	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr3:112125200-112126400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr3:112125400-112126000	Flanking Active TSS	GM12878-XiMat	blood
25	chr3:112125400-112126400	Enhancers	Brain Anterior Caudate	brain
26	chr3:112125400-112126600	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:112125400-112126600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr3:112125400-112126600	Enhancers	Brain Substantia Nigra	brain
29	chr3:112125400-112130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:112125400-112132200	Weak transcription	Placenta	Placenta

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