Variant report

Variant	rs2647256
Chromosome Location	chr4:106201556-106201557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10010281	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs10014102	0.80[YRI][hapmap]
rs10022109	1.00[YRI][hapmap]
rs1015521	0.87[JPT][hapmap]
rs12645165	0.80[YRI][hapmap]
rs12647922	1.00[ASW][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs13143564	1.00[MKK][hapmap]
rs1391438	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1391441	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs17583558	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17617028	1.00[YRI][hapmap]
rs2047408	0.87[JPT][hapmap]
rs2285720	0.80[YRI][hapmap]
rs2647230	0.85[ASN][1000 genomes]
rs2647243	0.81[ASN][1000 genomes]
rs2647249	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2726458	0.82[ASN][1000 genomes]
rs2726461	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2726492	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2726518	0.81[ASN][1000 genomes]
rs28493806	0.83[ASN][1000 genomes]
rs2903386	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs35515350	0.85[ASN][1000 genomes]
rs6533182	0.81[ASN][1000 genomes]
rs7655890	0.87[JPT][hapmap]
rs9790517	1.00[YRI][hapmap]
rs9884482	0.80[YRI][hapmap]
rs988799	0.90[CHB][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs992493	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879698	chr4:106155751-106309224	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2647256	OSTC	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106187200-106202000	Weak transcription	Stomach Mucosa	stomach
2	chr4:106196600-106202000	Weak transcription	Psoas Muscle	Psoas
3	chr4:106197400-106201600	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:106197400-106201800	Weak transcription	NHEK	skin
5	chr4:106197400-106202000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:106197400-106210200	Weak transcription	Small Intestine	intestine
7	chr4:106197600-106202000	Weak transcription	Aorta	Aorta
8	chr4:106197600-106204000	Weak transcription	Fetal Intestine Small	intestine
9	chr4:106197800-106202000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:106197800-106202000	Weak transcription	Adipose Nuclei	Adipose
11	chr4:106197800-106202000	Weak transcription	Brain Anterior Caudate	brain
12	chr4:106197800-106202000	Weak transcription	Pancreas	Pancrea
13	chr4:106197800-106202000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:106197800-106202200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:106197800-106202800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:106197800-106203200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:106197800-106204000	Weak transcription	Primary T cells from cord blood	blood
18	chr4:106197800-106204000	Weak transcription	Fetal Kidney	kidney
19	chr4:106198000-106201600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:106198000-106201800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:106198000-106201800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:106198000-106201800	Weak transcription	Brain Substantia Nigra	brain
23	chr4:106198000-106201800	Weak transcription	Right Ventricle	heart
24	chr4:106198000-106201800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:106198000-106202000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:106198000-106202000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:106198000-106202000	Weak transcription	Lung	lung
28	chr4:106198000-106202000	Weak transcription	Ovary	ovary
29	chr4:106198000-106202800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr4:106198000-106203200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:106198000-106204600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:106198000-106210600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:106198000-106210800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:106198200-106201600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:106198400-106203800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr4:106198600-106202000	Weak transcription	Fetal Thymus	thymus
37	chr4:106198600-106211800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:106198800-106201800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:106199000-106201600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:106199000-106201800	Weak transcription	Fetal Intestine Large	intestine
41	chr4:106199000-106203800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr4:106199200-106201600	Weak transcription	Brain Germinal Matrix	brain
43	chr4:106199200-106202000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:106199200-106202000	Weak transcription	Left Ventricle	heart
45	chr4:106199200-106202000	Weak transcription	HSMM	muscle
46	chr4:106199800-106201600	Weak transcription	GM12878-XiMat	blood
47	chr4:106200600-106203000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:106200800-106204600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:106201000-106202600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:106201000-106202600	Enhancers	NHDF-Ad	bronchial

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