Variant report

Variant	rs2633541
Chromosome Location	chr3:112125889-112125890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996724	1.00[ASN][1000 genomes]
rs2029318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087259	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129856	1.00[AFR][1000 genomes];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]
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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633606	1.00[AFR][1000 genomes];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	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	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683898	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:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:34 , 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	chr3:112118600-112130400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:112120800-112126600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:112122000-112126600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:112122400-112126000	Weak transcription	Fetal Intestine Large	intestine
7	chr3:112122400-112126200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:112123600-112126800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:112123800-112128800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:112124000-112126200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr3:112124400-112126200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:112124400-112127000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr3:112124800-112126400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:112124800-112127000	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:112124800-112127400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:112125000-112126000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:112125000-112126200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:112125200-112126400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr3:112125400-112126000	Flanking Active TSS	GM12878-XiMat	blood
20	chr3:112125400-112126400	Enhancers	Brain Anterior Caudate	brain
21	chr3:112125400-112126600	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:112125400-112126600	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr3:112125400-112126600	Enhancers	Brain Substantia Nigra	brain
24	chr3:112125400-112130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:112125400-112132200	Weak transcription	Placenta	Placenta
26	chr3:112125600-112126200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr3:112125600-112126400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:112125600-112126400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr3:112125600-112126600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:112125800-112126000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr3:112125800-112126200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:112125800-112126800	Enhancers	Primary B cells from cord blood	blood
33	chr3:112125800-112126800	Enhancers	Fetal Intestine Small	intestine
34	chr3:112125800-112127800	Enhancers	Duodenum Mucosa	Duodenum

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