Variant report

Variant	rs342056
Chromosome Location	chr2:20652507-20652508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20652177..20652961-chr2:20696034..20696726,2	MCF-7	breast:
2	chr2:20633992..20655025-chr2:20829429..20854651,127	MCF-7	breast:
3	chr2:20651983..20652871-chr2:20835232..20836648,4	MCF-7	breast:
4	chr2:20652012..20652879-chr2:20841845..20842518,4	MCF-7	breast:
5	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
6	chr2:20651129..20653256-chr2:20748051..20749784,2	MCF-7	breast:
7	chr2:20652225..20654236-chr2:20656975..20659900,2	K562	blood:
8	chr2:20651875..20654191-chr2:20757660..20759690,2	MCF-7	breast:
9	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
10	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
11	chr2:20652339..20652876-chr2:20724728..20725598,3	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RHOB-1	chr2:20651697-20654380	NONHSAT069442
2	lnc-RHOB-1	chr2:20650311-20652994	FPKM1_group_15529_transcript_1

No data

Variant related genes	Relation type
ENSG00000118960	Chromatin interaction
ENSG00000231948	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2602160	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2924378	0.83[ASN][1000 genomes]
rs342054	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs342055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][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	nsv455830	chr2:20621404-20659862	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv581166	chr2:20621404-20659862	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
3	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
8	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
9	nsv873722	chr2:20652507-20705910	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs342056	VSNL1	cis	parietal	SCAN
rs342056	FAM49A	cis	cerebellum	SCAN
rs342056	SMC6	cis	cerebellum	SCAN
rs342056	AC023137.2	cis	Artery Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20649800-20653000	Flanking Active TSS	Brain Anterior Caudate	brain
2	chr2:20649800-20653000	Enhancers	Placenta	Placenta
3	chr2:20650200-20652600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:20650400-20653000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:20650400-20653200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:20650600-20652600	Enhancers	Fetal Stomach	stomach
7	chr2:20650600-20652800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:20650600-20652800	Enhancers	HepG2	liver
9	chr2:20650600-20653200	Enhancers	Colon Smooth Muscle	Colon
10	chr2:20650800-20652600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:20650800-20653000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:20650800-20656000	Weak transcription	NHLF	lung
13	chr2:20650800-20659000	Weak transcription	Pancreas	Pancrea
14	chr2:20651000-20652800	Enhancers	HUVEC	blood vessel
15	chr2:20651000-20653200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:20651000-20655000	Weak transcription	Fetal Brain Female	brain
17	chr2:20651200-20653000	Enhancers	Rectal Smooth Muscle	rectum
18	chr2:20651200-20653400	Enhancers	Brain Angular Gyrus	brain
19	chr2:20651200-20654200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:20651200-20655800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:20651200-20656000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:20651200-20656000	Weak transcription	NH-A	brain
23	chr2:20651400-20652800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:20651400-20653400	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:20651400-20653400	Enhancers	Brain Substantia Nigra	brain
26	chr2:20651400-20655600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:20651400-20655800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:20651400-20656000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:20651400-20656000	Weak transcription	NHDF-Ad	bronchial
30	chr2:20651400-20656600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:20651600-20653200	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:20651600-20656200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:20651600-20656600	Weak transcription	HSMM	muscle
34	chr2:20651800-20652600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:20652000-20652600	Enhancers	Esophagus	oesophagus
36	chr2:20652000-20652600	Enhancers	Ovary	ovary
37	chr2:20652000-20652800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:20652000-20652800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:20652000-20652800	Enhancers	Stomach Smooth Muscle	stomach
40	chr2:20652200-20652600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
41	chr2:20652200-20652800	Weak transcription	Fetal Brain Male	brain
42	chr2:20652200-20653400	Enhancers	Brain Hippocampus Middle	brain
43	chr2:20652200-20655000	Weak transcription	Psoas Muscle	Psoas
44	chr2:20652200-20655400	Weak transcription	Right Atrium	heart
45	chr2:20652200-20655800	Weak transcription	Aorta	Aorta
46	chr2:20652400-20657000	Weak transcription	Osteobl	bone

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