Variant report

Variant	rs323880
Chromosome Location	chr3:51985956-51985957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51985563..51987517-chr3:51990241..51992502,2	MCF-7	breast:
2	chr3:51972961..51975805-chr3:51984917..51986970,2	MCF-7	breast:
3	chr3:51982600..51984410-chr3:51985795..51988136,2	K562	blood:
4	chr3:51983749..51985969-chr3:52006072..52007842,2	K562	blood:
5	chr3:51985305..51989166-chr3:51989564..51992012,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCBP4-2	chr3:51985865-51987918	NONHSAT089889

Variant related genes	Relation type
ENSG00000248487	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs178918	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323869	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323870	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323872	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323878	1.00[AMR][1000 genomes]
rs323889	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323891	1.00[AMR][1000 genomes]
rs323896	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323900	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368210	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs422304	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56746340	1.00[AMR][1000 genomes]
rs57384151	1.00[AMR][1000 genomes]
rs6446141	1.00[AMR][1000 genomes]
rs72961930	1.00[AMR][1000 genomes]
rs72961999	1.00[AMR][1000 genomes]
rs72964016	1.00[AMR][1000 genomes]
rs7426999	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7636204	1.00[AMR][1000 genomes]
rs9683234	1.00[AMR][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	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51977200-51987600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:51977200-51989200	Weak transcription	Ovary	ovary
3	chr3:51977200-51992000	Weak transcription	Aorta	Aorta
4	chr3:51977400-51986200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:51977400-51987200	Weak transcription	Fetal Lung	lung
6	chr3:51977400-51989200	Weak transcription	Esophagus	oesophagus
7	chr3:51977600-51986000	Weak transcription	Fetal Intestine Large	intestine
8	chr3:51977600-51987200	Weak transcription	HSMMtube	muscle
9	chr3:51977600-51987600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:51977600-51987600	Weak transcription	HSMM	muscle
11	chr3:51977600-51989000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:51977600-51989000	Weak transcription	Pancreas	Pancrea
13	chr3:51977600-51989400	Weak transcription	Left Ventricle	heart
14	chr3:51977800-51986000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:51977800-51987200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:51977800-51987800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:51977800-51989400	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:51978800-51987000	Weak transcription	Hela-S3	cervix
19	chr3:51979000-51987200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:51979200-51986000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:51979800-51987200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:51980400-51989400	Weak transcription	Right Ventricle	heart
23	chr3:51980600-51989200	Weak transcription	Gastric	stomach
24	chr3:51980800-51987200	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:51980800-51988000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:51982400-51987400	Weak transcription	Fetal Intestine Small	intestine
27	chr3:51982400-51987800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:51982600-51986200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:51982600-51986600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:51983000-51987200	Weak transcription	Osteobl	bone
31	chr3:51983400-51987000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:51983400-51988400	Weak transcription	Colonic Mucosa	Colon
33	chr3:51983400-51989000	Weak transcription	Brain Anterior Caudate	brain
34	chr3:51983400-51989000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:51983400-51989000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:51983400-51989400	Weak transcription	Lung	lung
37	chr3:51983600-51986000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:51983600-51986600	Weak transcription	Fetal Stomach	stomach
39	chr3:51983600-51987200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:51983600-51987200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:51983600-51987400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:51983600-51987800	Weak transcription	NHLF	lung
43	chr3:51983600-51989000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:51983600-51989200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:51983600-51989200	Weak transcription	Adipose Nuclei	Adipose
46	chr3:51983600-51989200	Weak transcription	Spleen	Spleen
47	chr3:51983800-51987200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:51983800-51987200	Weak transcription	Brain Angular Gyrus	brain
49	chr3:51983800-51990200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:51984000-51987000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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