Variant report

Variant	rs500936
Chromosome Location	chr1:103240428-103240429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1932342	0.83[EUR][1000 genomes]
rs2199554	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2199555	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708397	0.82[EUR][1000 genomes]
rs2708398	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471949	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472765	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs479990	0.91[AFR][1000 genomes]
rs511308	0.84[EUR][1000 genomes]
rs514077	0.84[EUR][1000 genomes]
rs514099	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520747	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs570092	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579692	0.84[EUR][1000 genomes]
rs597499	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618072	0.84[EUR][1000 genomes]
rs620658	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629282	0.84[EUR][1000 genomes]
rs631137	0.84[EUR][1000 genomes]
rs665275	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs674479	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687616	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs688880	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462705	chr1:103123803-103267759	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv546923	chr1:103123803-103267759	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv870987	chr1:103155901-103267759	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv462716	chr1:103176592-103259724	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv546924	chr1:103176592-103259724	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv546925	chr1:103176592-103267759	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv546926	chr1:103183066-103267759	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv830882	chr1:103192683-103355802	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv546927	chr1:103199589-103267759	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3403184	chr1:103238964-103241087	Active TSS Flanking Active TSS Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
11	esv3355649	chr1:103239464-103240612	Active TSS Flanking Active TSS Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103233200-103243200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:103238600-103241600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:103240000-103240800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:103240000-103240800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:103240000-103241000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:103240200-103240600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:103240200-103240600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:103240200-103240600	Active TSS	Brain Hippocampus Middle	brain
9	chr1:103240200-103240600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr1:103240200-103240600	Active TSS	Brain Substantia Nigra	brain
11	chr1:103240200-103240600	Active TSS	Psoas Muscle	Psoas
12	chr1:103240200-103240600	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr1:103240200-103240600	Active TSS	Hela-S3	cervix
14	chr1:103240200-103240600	Active TSS	HMEC	breast
15	chr1:103240200-103240600	Active TSS	HSMMtube	muscle
16	chr1:103240200-103240600	Active TSS	HUVEC	blood vessel
17	chr1:103240200-103240800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:103240200-103240800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:103240200-103240800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:103240200-103240800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:103240200-103240800	Active TSS	Muscle Satellite Cultured Cells	--
22	chr1:103240200-103240800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:103240200-103240800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:103240200-103240800	Active TSS	Brain Angular Gyrus	brain
25	chr1:103240200-103240800	Active TSS	Fetal Muscle Leg	muscle
26	chr1:103240200-103240800	Active TSS	Ovary	ovary
27	chr1:103240200-103240800	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:103240200-103240800	Active TSS	Rectal Smooth Muscle	rectum
29	chr1:103240200-103240800	Active TSS	Stomach Smooth Muscle	stomach
30	chr1:103240200-103240800	Active TSS	A549	lung
31	chr1:103240200-103240800	Active TSS	HSMM	muscle
32	chr1:103240200-103240800	Active TSS	Osteobl	bone
33	chr1:103240200-103241000	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr1:103240400-103240600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:103240400-103240600	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr1:103240400-103240600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:103240400-103240600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:103240400-103240600	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:103240400-103240800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:103240400-103240800	Active TSS	Adipose Nuclei	Adipose
41	chr1:103240400-103240800	Active TSS	Pancreas	Pancrea
42	chr1:103240400-103240800	Active TSS	Right Atrium	heart
43	chr1:103240400-103240800	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr1:103240400-103240800	Active TSS	NHDF-Ad	bronchial
45	chr1:103240400-103241000	Enhancers	HUES6 Cell Line	embryonic stem cell

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