Variant report

Variant	rs62250902
Chromosome Location	chr3:53842251-53842252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53841128..53843687-chr3:53845515..53847366,2	K562	blood:
2	chr3:53841487..53843004-chr3:53876631..53879451,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000016391	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10154841	0.83[ASN][1000 genomes]
rs10490844	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62250930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1003204	chr3:53820070-53877149	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1002375	chr3:53822319-53872753	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53811600-53843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:53829200-53853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:53830400-53851200	Weak transcription	Fetal Brain Male	brain
4	chr3:53838400-53842400	Enhancers	Fetal Heart	heart
5	chr3:53839000-53849800	Strong transcription	Fetal Lung	lung
6	chr3:53839200-53855200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:53839400-53851400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:53839600-53849000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:53839600-53851000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:53839600-53851200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:53839600-53852800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:53839600-53876600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:53839800-53843800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:53839800-53849200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:53840600-53844000	Weak transcription	Lung	lung
16	chr3:53840600-53851200	Weak transcription	Aorta	Aorta
17	chr3:53840800-53853600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:53841000-53852600	Weak transcription	Ovary	ovary
19	chr3:53841000-53852800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:53841200-53843200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:53841200-53845200	Weak transcription	Gastric	stomach
22	chr3:53841400-53842600	Weak transcription	Spleen	Spleen
23	chr3:53841400-53849000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:53841400-53850400	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:53841600-53843000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:53841600-53844800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:53841600-53849000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:53841600-53851000	Weak transcription	Brain Angular Gyrus	brain
29	chr3:53841600-53851200	Weak transcription	Colonic Mucosa	Colon
30	chr3:53841600-53851400	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:53841600-53851400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:53841600-53855600	Weak transcription	Right Ventricle	heart
33	chr3:53841600-53855800	Weak transcription	Right Atrium	heart
34	chr3:53841800-53850600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:53841800-53850600	Weak transcription	HepG2	liver
36	chr3:53841800-53851200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:53841800-53853400	Weak transcription	Fetal Brain Female	brain
38	chr3:53841800-53853400	Weak transcription	GM12878-XiMat	blood
39	chr3:53842200-53844200	Weak transcription	Pancreas	Pancrea
40	chr3:53842200-53852200	Strong transcription	Fetal Intestine Small	intestine
41	chr3:53842200-53852600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:53842200-53857200	Strong transcription	Fetal Intestine Large	intestine

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