Variant report

Variant	rs17828225
Chromosome Location	chr2:58110236-58110237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:58108798..58111320-chr2:58112288..58115523,3	K562	blood:
2	chr2:58107882..58110920-chr2:58111613..58114646,4	MCF-7	breast:
3	chr2:58109065..58111032-chr2:58113088..58114709,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10179365	0.94[ASN][1000 genomes]
rs10187670	0.89[ASN][1000 genomes]
rs10197268	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887238	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13384219	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13405071	0.94[ASN][1000 genomes]
rs17231440	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73942239	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv874196	chr2:57946148-58220320	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834148	chr2:57979661-58119213	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1010981	chr2:58013389-58205699	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv874199	chr2:58031249-58161520	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 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	chr2:58106000-58113000	Weak transcription	Brain Germinal Matrix	brain
2	chr2:58106000-58113400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:58106000-58113400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:58106000-58113400	Weak transcription	Pancreas	Pancrea
5	chr2:58106400-58113600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:58108000-58110600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:58108000-58110600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:58108000-58110600	Flanking Active TSS	GM12878-XiMat	blood
9	chr2:58108600-58110400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr2:58108600-58111600	Weak transcription	Fetal Brain Female	brain
11	chr2:58108800-58110400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr2:58108800-58110400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr2:58109000-58110400	Enhancers	HSMMtube	muscle
14	chr2:58109200-58110400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:58109200-58110600	Active TSS	A549	lung
16	chr2:58109400-58110400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:58109400-58110400	Flanking Active TSS	Osteobl	bone
18	chr2:58109400-58110600	Active TSS	Brain Cingulate Gyrus	brain
19	chr2:58109400-58110600	Active TSS	Brain Hippocampus Middle	brain
20	chr2:58109400-58110600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr2:58109600-58110600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr2:58109600-58110600	Active TSS	Brain Angular Gyrus	brain
23	chr2:58109600-58110600	Active TSS	Brain Anterior Caudate	brain
24	chr2:58109600-58110600	Active TSS	Brain Substantia Nigra	brain
25	chr2:58109600-58110600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr2:58109800-58110400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:58109800-58110400	Active TSS	Rectal Smooth Muscle	rectum
28	chr2:58109800-58110400	Flanking Active TSS	NHDF-Ad	bronchial
29	chr2:58109800-58110600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:58109800-58110600	Active TSS	Stomach Smooth Muscle	stomach
31	chr2:58110000-58110400	Active TSS	Duodenum Mucosa	Duodenum
32	chr2:58110000-58110400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr2:58110000-58110400	Enhancers	Fetal Brain Male	brain
34	chr2:58110000-58110400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr2:58110000-58110400	Active TSS	Right Atrium	heart
36	chr2:58110000-58110400	Active TSS	K562	blood
37	chr2:58110000-58110400	Active TSS	NHLF	lung
38	chr2:58110000-58113400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:58110200-58110400	Flanking Active TSS	Ovary	ovary
40	chr2:58110200-58110400	Active TSS	HepG2	liver
41	chr2:58110200-58110600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr2:58110200-58111000	Enhancers	Hela-S3	cervix

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