Variant report

Variant	rs4257409
Chromosome Location	chr2:112853913-112853914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112849302..112851484-chr2:112851521..112855530,4	K562	blood:
2	chr2:112844930..112847858-chr2:112851093..112855294,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153214	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10165845	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175143	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178449	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182333	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045300	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779884	0.97[ASN][1000 genomes]
rs10864898	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618637	0.90[ASN][1000 genomes]
rs4241121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4613287	0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4848993	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849007	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849044	0.90[ASN][1000 genomes]
rs6707397	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs6730057	0.98[ASN][1000 genomes]
rs6731563	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737707	0.86[CHD][hapmap];0.83[MEX][hapmap]
rs7577442	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7580507	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581849	0.90[JPT][hapmap]
rs7591702	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595574	0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308669	0.87[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653401	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653422	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	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
rs4257409	POLR1B	cis	parietal	SCAN
rs4257409	CCDC138	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112814200-112859800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:112816600-112866200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:112816800-112871400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr2:112822200-112854400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:112822800-112876800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:112832000-112866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:112833600-112855800	Weak transcription	Hela-S3	cervix
8	chr2:112834600-112871200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr2:112835800-112883200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:112836000-112874400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:112838200-112866200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr2:112838200-112866400	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:112838600-112858200	Strong transcription	Fetal Intestine Large	intestine
14	chr2:112843000-112869400	Weak transcription	Fetal Heart	heart
15	chr2:112845000-112856200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:112845200-112856000	Weak transcription	Fetal Brain Male	brain
17	chr2:112845400-112856000	Weak transcription	Brain Substantia Nigra	brain
18	chr2:112845400-112856200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:112845400-112875200	Weak transcription	Right Ventricle	heart
20	chr2:112845600-112856000	Weak transcription	Ovary	ovary
21	chr2:112845600-112856400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:112845600-112865400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:112845800-112855400	Weak transcription	Small Intestine	intestine
24	chr2:112845800-112856200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:112846000-112856200	Weak transcription	Fetal Brain Female	brain
26	chr2:112846000-112856400	Weak transcription	Brain Germinal Matrix	brain
27	chr2:112846200-112854600	Strong transcription	Primary B cells from cord blood	blood
28	chr2:112846200-112865800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:112847000-112855400	Weak transcription	Colonic Mucosa	Colon
30	chr2:112847800-112854000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:112847800-112856000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:112847800-112856000	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:112847800-112856200	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:112847800-112856400	Weak transcription	Brain Angular Gyrus	brain
35	chr2:112847800-112867200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:112848000-112856200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:112848200-112856000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:112848200-112856000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:112848200-112856000	Weak transcription	Fetal Kidney	kidney
40	chr2:112848200-112856200	Weak transcription	Brain Anterior Caudate	brain
41	chr2:112848200-112856400	Weak transcription	Aorta	Aorta
42	chr2:112848400-112856400	Weak transcription	A549	lung
43	chr2:112849200-112854200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:112849400-112855800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:112850200-112856200	Weak transcription	HMEC	breast
46	chr2:112850400-112854000	Genic enhancers	HUVEC	blood vessel
47	chr2:112850400-112856200	Weak transcription	Lung	lung
48	chr2:112850400-112856400	Weak transcription	Spleen	Spleen
49	chr2:112851000-112855600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:112851000-112866400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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