Variant report

Variant	rs28654487
Chromosome Location	chr2:56676604-56676605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10165672	1.00[EUR][1000 genomes]
rs10165892	1.00[EUR][1000 genomes]
rs10166050	1.00[EUR][1000 genomes]
rs10176983	1.00[EUR][1000 genomes]
rs10180194	1.00[EUR][1000 genomes]
rs10181815	1.00[EUR][1000 genomes]
rs10183259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10193624	1.00[EUR][1000 genomes]
rs10193747	1.00[EUR][1000 genomes]
rs10198440	1.00[EUR][1000 genomes]
rs10200031	1.00[EUR][1000 genomes]
rs10202374	1.00[EUR][1000 genomes]
rs11887424	1.00[EUR][1000 genomes]
rs11896577	1.00[EUR][1000 genomes]
rs11897129	1.00[EUR][1000 genomes]
rs13384989	1.00[EUR][1000 genomes]
rs13386727	1.00[EUR][1000 genomes]
rs13387143	1.00[EUR][1000 genomes]
rs13396144	1.00[EUR][1000 genomes]
rs13398609	1.00[EUR][1000 genomes]
rs13401849	1.00[EUR][1000 genomes]
rs13407738	1.00[EUR][1000 genomes]
rs13408350	1.00[EUR][1000 genomes]
rs13411174	1.00[EUR][1000 genomes]
rs13412157	1.00[EUR][1000 genomes]
rs13417902	1.00[EUR][1000 genomes]
rs13421608	1.00[EUR][1000 genomes]
rs13431398	1.00[EUR][1000 genomes]
rs17047938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17047945	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17048166	1.00[EUR][1000 genomes]
rs17048167	1.00[EUR][1000 genomes]
rs17048189	1.00[EUR][1000 genomes]
rs17048223	1.00[EUR][1000 genomes]
rs2081427	1.00[EUR][1000 genomes]
rs2193483	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2194793	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2216493	1.00[EUR][1000 genomes]
rs28530709	0.89[AMR][1000 genomes]
rs28678883	1.00[EUR][1000 genomes]
rs55923854	1.00[EUR][1000 genomes]
rs59956872	1.00[EUR][1000 genomes]
rs6741874	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73940723	1.00[EUR][1000 genomes]
rs73940724	1.00[EUR][1000 genomes]
rs73940726	1.00[EUR][1000 genomes]
rs7556872	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7559732	1.00[EUR][1000 genomes]
rs7570781	1.00[EUR][1000 genomes]
rs7586424	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834093	chr2:56538097-56708677	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1004449	chr2:56538460-56715861	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv874171	chr2:56545845-56727178	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv522944	chr2:56603985-56676997	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv874172	chr2:56638856-56811749	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2757800	chr2:56659685-56851198	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2759052	chr2:56659685-56851198	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56674400-56678200	Enhancers	Fetal Intestine Large	intestine
2	chr2:56675000-56677800	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr2:56675000-56677800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr2:56675200-56677000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr2:56675200-56678000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr2:56675400-56676800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:56675400-56677000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr2:56675400-56677000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr2:56675400-56677200	Enhancers	Liver	Liver
10	chr2:56675400-56678200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr2:56675400-56679200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:56675600-56677000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:56675600-56677000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr2:56675600-56677000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:56675600-56677000	Flanking Active TSS	A549	lung
16	chr2:56675800-56676800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:56675800-56676800	Weak transcription	Psoas Muscle	Psoas
18	chr2:56675800-56677000	Enhancers	Fetal Muscle Leg	muscle
19	chr2:56675800-56677000	Enhancers	Gastric	stomach
20	chr2:56676000-56676800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:56676000-56676800	Active TSS	Duodenum Mucosa	Duodenum
22	chr2:56676000-56677000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:56676000-56677000	Weak transcription	Stomach Mucosa	stomach
24	chr2:56676000-56682800	Weak transcription	Pancreas	Pancrea
25	chr2:56676200-56676800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr2:56676400-56676800	Flanking Active TSS	Fetal Intestine Small	intestine
27	chr2:56676600-56676800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr2:56676600-56676800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:56676600-56676800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr2:56676600-56677000	Enhancers	HepG2	liver
31	chr2:56676600-56677200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:56676600-56677800	Enhancers	Fetal Kidney	kidney

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