Variant report

Variant	rs2289225
Chromosome Location	chr2:190323376-190323377
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	chr2:190314612..190317540-chr2:190321508..190324185,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10497701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497702	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs1123109	1.00[ASW][hapmap]
rs11568351	1.00[ASW][hapmap]
rs11681937	1.00[AFR][1000 genomes]
rs11686908	0.94[ASN][1000 genomes]
rs11688806	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1371470	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1402369	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17198857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17198892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271015	1.00[AFR][1000 genomes]
rs17271036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17271043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271071	0.92[ASN][1000 genomes]
rs17271183	1.00[ASW][hapmap]
rs2304701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55822942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58584769	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58926658	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61410845	0.90[ASN][1000 genomes]
rs62182066	1.00[AFR][1000 genomes]
rs62182070	0.90[ASN][1000 genomes]
rs62184647	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62184648	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62184649	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62184652	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62184653	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62187072	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62187074	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62187075	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62187077	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62187078	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62187082	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62187106	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6721290	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6747132	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72914141	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs72914144	1.00[AFR][1000 genomes]
rs72914175	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7423067	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2289225	COL5A2	cis	parietal	SCAN
rs2289225	COL5A2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190306800-190323800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:190306800-190344200	Weak transcription	Esophagus	oesophagus
3	chr2:190307000-190334200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:190307600-190323400	Weak transcription	Ovary	ovary
5	chr2:190307600-190330000	Weak transcription	Fetal Heart	heart
6	chr2:190307600-190334200	Weak transcription	Pancreas	Pancrea
7	chr2:190307600-190338200	Weak transcription	Spleen	Spleen
8	chr2:190307600-190342000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:190307600-190342600	Weak transcription	Aorta	Aorta
10	chr2:190307800-190332400	Weak transcription	Stomach Mucosa	stomach
11	chr2:190308000-190334600	Weak transcription	Right Ventricle	heart
12	chr2:190308200-190325000	Weak transcription	Thymus	Thymus
13	chr2:190308200-190328400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:190308200-190328600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:190308200-190342800	Strong transcription	A549	lung
16	chr2:190308400-190329800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:190308600-190341800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:190308600-190342200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:190309000-190342600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:190309200-190327600	Weak transcription	Psoas Muscle	Psoas
21	chr2:190309200-190341200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:190309400-190337200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:190309600-190325600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:190309600-190341800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:190309600-190342000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:190309800-190326400	Strong transcription	Fetal Intestine Large	intestine
27	chr2:190309800-190337000	Strong transcription	Primary B cells from cord blood	blood
28	chr2:190309800-190342400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:190310200-190340600	Strong transcription	Dnd41	blood
30	chr2:190310200-190341600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:190310400-190325000	Strong transcription	Primary T cells from cord blood	blood
32	chr2:190310400-190341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:190310800-190342000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:190310800-190342000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:190311000-190340400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:190311000-190341600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:190311000-190341800	Strong transcription	NH-A	brain
38	chr2:190311200-190323600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:190311200-190341800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr2:190311600-190341800	Strong transcription	HMEC	breast
41	chr2:190311800-190341400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:190311800-190342400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:190312000-190325400	Strong transcription	HUVEC	blood vessel
44	chr2:190312000-190341600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:190312200-190325400	Strong transcription	Fetal Brain Female	brain
46	chr2:190312200-190325800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:190312200-190330200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr2:190312200-190335600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:190312200-190336400	Strong transcription	Placenta	Placenta
50	chr2:190312200-190339600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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