Variant report

Variant	rs1997113
Chromosome Location	chr2:39694812-39694813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39673263..39677123-chr2:39692250..39696646,6	MCF-7	breast:
2	chr2:39694431..39697205-chr2:39730797..39733915,4	MCF-7	breast:
3	chr2:39694399..39696042-chr2:39720028..39722493,2	K562	blood:
4	chr2:39685470..39688702-chr2:39694435..39696630,3	MCF-7	breast:
5	chr2:39662686..39670121-chr2:39690503..39697386,20	MCF-7	breast:
6	chr2:39663070..39666737-chr2:39691085..39694878,4	MCF-7	breast:
7	chr2:39692371..39695353-chr2:39710610..39713558,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10164629	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10184116	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1060691	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10865153	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11124685	0.85[CEU][hapmap]
rs11680511	0.80[AMR][1000 genomes]
rs12712644	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13024956	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2287089	0.85[ASN][1000 genomes]
rs62136541	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719503	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6738090	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6747519	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7573541	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9677244	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39665200-39696000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39666200-39696600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:39667200-39696400	Weak transcription	Fetal Heart	heart
4	chr2:39668200-39696800	Weak transcription	Right Ventricle	heart
5	chr2:39675000-39696400	Weak transcription	Fetal Kidney	kidney
6	chr2:39678000-39696800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:39682200-39695600	Weak transcription	Fetal Brain Male	brain
8	chr2:39682600-39695600	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:39682600-39695800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:39685200-39705000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:39685800-39696000	Weak transcription	Left Ventricle	heart
12	chr2:39687400-39695200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:39688600-39703400	Weak transcription	Liver	Liver
14	chr2:39691000-39695800	Weak transcription	Brain Anterior Caudate	brain
15	chr2:39691400-39695600	Weak transcription	Fetal Stomach	stomach
16	chr2:39692400-39695000	Weak transcription	Fetal Lung	lung
17	chr2:39692600-39696800	Weak transcription	Spleen	Spleen
18	chr2:39693000-39697000	Weak transcription	Lung	lung
19	chr2:39693200-39697200	Enhancers	Stomach Mucosa	stomach
20	chr2:39693800-39698000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:39694400-39695200	Enhancers	Psoas Muscle	Psoas
22	chr2:39694400-39696600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:39694400-39696800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:39694400-39696800	Enhancers	HepG2	liver
25	chr2:39694400-39697000	Enhancers	NHDF-Ad	bronchial
26	chr2:39694400-39697400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:39694400-39697400	Enhancers	Placenta	Placenta
28	chr2:39694400-39697600	Enhancers	GM12878-XiMat	blood
29	chr2:39694600-39695400	Enhancers	Duodenum Mucosa	Duodenum
30	chr2:39694600-39695600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:39694600-39695600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:39694600-39695600	Enhancers	Hela-S3	cervix
33	chr2:39694600-39696200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr2:39694600-39696400	Enhancers	A549	lung
35	chr2:39694600-39696600	Enhancers	Stomach Smooth Muscle	stomach
36	chr2:39694600-39696800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:39694600-39696800	Enhancers	NHLF	lung
38	chr2:39694600-39696800	Enhancers	Osteobl	bone
39	chr2:39694600-39697000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr2:39694600-39697200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:39694600-39697200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:39694600-39697200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr2:39694600-39697400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:39694600-39697400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:39694600-39697400	Enhancers	Fetal Intestine Large	intestine
46	chr2:39694600-39697400	Enhancers	Ovary	ovary
47	chr2:39694600-39697400	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr2:39694600-39697400	Enhancers	Rectal Smooth Muscle	rectum
49	chr2:39694600-39697400	Enhancers	Right Atrium	heart
50	chr2:39694600-39697400	Enhancers	HSMM	muscle

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