Variant report

Variant	rs6594681
Chromosome Location	chr5:112439941-112439942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12108764	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1562017	1.00[YRI][hapmap]
rs33555	1.00[CHB][hapmap]
rs4235782	0.83[AFR][1000 genomes]
rs4374752	1.00[YRI][hapmap]
rs4397122	1.00[AFR][1000 genomes]
rs4705540	1.00[AFR][1000 genomes]
rs4705764	1.00[YRI][hapmap]
rs4705771	1.00[AFR][1000 genomes]
rs6594657	1.00[YRI][hapmap]
rs6594666	1.00[YRI][hapmap]
rs6862944	1.00[YRI][hapmap]
rs6881233	1.00[YRI][hapmap]
rs6881477	1.00[YRI][hapmap]
rs6882115	1.00[YRI][hapmap]
rs6894711	0.83[AFR][1000 genomes]
rs6895843	1.00[YRI][hapmap]
rs6898395	1.00[AFR][1000 genomes]
rs7729027	1.00[AFR][1000 genomes]
rs7729055	1.00[AFR][1000 genomes]
rs878074	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112399800-112441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:112411200-112443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:112418400-112441600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:112418600-112441400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:112424400-112448000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:112426000-112441600	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:112426200-112445000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:112426600-112453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:112426800-112450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
12	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
14	chr5:112427000-112440800	Weak transcription	NH-A	brain
15	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
16	chr5:112427200-112448200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:112427600-112441600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:112427600-112442000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:112427600-112443200	Weak transcription	Brain Substantia Nigra	brain
20	chr5:112428000-112440200	Strong transcription	Liver	Liver
21	chr5:112428400-112440200	Strong transcription	Fetal Stomach	stomach
22	chr5:112428600-112445000	Weak transcription	Placenta	Placenta
23	chr5:112430400-112441000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:112431000-112440000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:112431000-112442600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:112431600-112440200	Strong transcription	Ovary	ovary
28	chr5:112432200-112443200	Weak transcription	Lung	lung
29	chr5:112432200-112450200	Weak transcription	Spleen	Spleen
30	chr5:112432200-112454600	Weak transcription	Pancreas	Pancrea
31	chr5:112433600-112441200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:112433800-112443800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:112436000-112442400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr5:112436400-112440600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr5:112436800-112441400	Strong transcription	NHEK	skin
37	chr5:112437000-112440200	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:112437600-112445800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:112437800-112454400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr5:112438000-112440200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:112438000-112444400	Weak transcription	HMEC	breast
42	chr5:112438000-112450600	Weak transcription	Aorta	Aorta
43	chr5:112438000-112454200	Weak transcription	Psoas Muscle	Psoas
44	chr5:112438200-112444800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:112438200-112450000	Weak transcription	Adipose Nuclei	Adipose
46	chr5:112438200-112450200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:112438200-112452800	Weak transcription	Brain Anterior Caudate	brain
48	chr5:112438400-112443000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:112438400-112443000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr5:112438800-112440200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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