Variant report

Variant	rs2129856
Chromosome Location	chr3:112115084-112115085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1386897	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586508	1.00[ASN][1000 genomes]
rs1872986	0.84[EUR][1000 genomes]
rs1872987	0.85[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996724	1.00[ASN][1000 genomes]
rs2029318	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087259	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244035	1.00[ASN][1000 genomes]
rs2263365	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633541	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[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]
rs2633591	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633595	1.00[ASN][1000 genomes]
rs2633601	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633607	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633608	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683890	0.85[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683896	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683897	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683898	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683901	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683902	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683903	1.00[EUR][1000 genomes]
rs2683904	1.00[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:9 , 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
7	esv3494206	chr3:112101762-112115260	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	n/a	n/a	inside rSNPs	n/a
8	esv3494204	chr3:112102212-112115110	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	n/a
9	nsv998316	chr3:112102565-112116643	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112107200-112117000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr3:112107400-112117000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:112110400-112115200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:112110600-112116600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:112110800-112118400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:112111400-112120400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:112111800-112125400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:112112200-112116400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:112112400-112116600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:112112400-112118000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:112112600-112116400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:112112800-112116800	Enhancers	Fetal Lung	lung
13	chr3:112112800-112117000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr3:112113000-112115400	Enhancers	HUVEC	blood vessel
15	chr3:112113000-112115600	Enhancers	Fetal Muscle Leg	muscle
16	chr3:112113000-112116600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:112113200-112116400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:112113200-112117000	Enhancers	Placenta	Placenta
19	chr3:112113400-112115200	Enhancers	Adipose Nuclei	Adipose
20	chr3:112113400-112116400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:112113400-112116400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:112113400-112116600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:112113400-112117800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:112113400-112124600	Weak transcription	HMEC	breast
25	chr3:112113600-112115200	Enhancers	Rectal Smooth Muscle	rectum
26	chr3:112113600-112116400	Weak transcription	Ovary	ovary
27	chr3:112113600-112116600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:112113600-112120600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:112114000-112115400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:112114000-112116600	Weak transcription	Lung	lung
31	chr3:112114200-112115400	Enhancers	Colon Smooth Muscle	Colon
32	chr3:112114400-112115200	Enhancers	Fetal Kidney	kidney
33	chr3:112114400-112116800	Enhancers	Primary hematopoietic stem cells	blood
34	chr3:112114600-112115200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:112114600-112116400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:112114600-112116600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:112114600-112116600	Weak transcription	Aorta	Aorta
38	chr3:112114800-112116000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr3:112114800-112116400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:112115000-112115400	Enhancers	Fetal Stomach	stomach
41	chr3:112115000-112116400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:112115000-112121200	Weak transcription	Rectal Mucosa Donor 29	rectum

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