Variant report

Variant	rs2255457
Chromosome Location	chr4:128554404-128554405
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174967985..174968897-chr4:128553828..128554517,2	Hela-S3	cervix:
2	chr4:128534491..128537175-chr4:128554257..128557179,2	MCF-7	breast:
3	chr4:128553197..128555974-chr4:128981706..128984336,2	K562	blood:
4	chr4:128543078..128545882-chr4:128552977..128554729,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116161	Chromatin interaction
ENSG00000164066	Chromatin interaction
ENSG00000138709	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1018289	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098931	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098933	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11728750	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11732886	0.92[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12509562	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12511932	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12649427	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12650360	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13126673	0.85[CEU][hapmap]
rs13151291	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1399210	0.87[EUR][1000 genomes]
rs1399211	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459049	0.81[CEU][hapmap]
rs1459051	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1514298	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1514299	0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs1913464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2048685	0.87[EUR][1000 genomes]
rs2048686	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2125573	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs2391188	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2391189	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28656192	0.85[EUR][1000 genomes]
rs34240473	0.94[ASN][1000 genomes]
rs36179490	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3749507	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs4543128	0.85[CEU][hapmap]
rs4833383	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs4834206	0.86[EUR][1000 genomes]
rs4834209	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4834210	0.81[CEU][hapmap]
rs4834211	0.85[CEU][hapmap];0.84[GIH][hapmap]
rs59255549	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62334037	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6534630	0.86[EUR][1000 genomes]
rs6534631	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534632	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs6534633	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6534634	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534637	0.85[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs6810904	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6823957	0.92[ASN][1000 genomes]
rs6828511	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847056	0.85[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs6847397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6858855	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7664217	0.88[EUR][1000 genomes]
rs7679782	0.80[EUR][1000 genomes]
rs7683627	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7686395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692114	0.89[CEU][hapmap]
rs922060	0.92[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1029214	chr4:128292215-128683123	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537247	chr4:128292215-128683123	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv879916	chr4:128422400-128694288	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1800085	chr4:128502675-128557864	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv830056	chr4:128517139-128676557	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv879918	chr4:128543742-128694288	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv879919	chr4:128543742-128697519	Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv879920	chr4:128554404-128694288	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv879921	chr4:128554404-128766074	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2255457	PGRMC2	cis	cerebellum	SCAN
rs2255457	LARP1B	cis	parietal	SCAN
rs2255457	HSPA4L	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128553000-128554800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:128553000-128555200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:128553200-128554800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:128553200-128555400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr4:128553200-128555800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr4:128553400-128554600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:128553400-128554600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
8	chr4:128553400-128554600	Active TSS	Fetal Heart	heart
9	chr4:128553400-128554600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr4:128553400-128554600	Bivalent/Poised TSS	HepG2	liver
11	chr4:128553400-128554800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr4:128553400-128554800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:128553400-128554800	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr4:128553400-128554800	Active TSS	Aorta	Aorta
15	chr4:128553400-128554800	Active TSS	Fetal Lung	lung
16	chr4:128553400-128554800	Active TSS	Fetal Muscle Leg	muscle
17	chr4:128553400-128554800	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr4:128553400-128554800	Active TSS	NH-A	brain
19	chr4:128553400-128555000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr4:128553400-128555000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:128553400-128555000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr4:128553400-128555000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:128553400-128555000	Active TSS	Brain Anterior Caudate	brain
24	chr4:128553400-128555000	Active TSS	Brain Cingulate Gyrus	brain
25	chr4:128553400-128555000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:128553400-128555000	Active TSS	Brain Substantia Nigra	brain
27	chr4:128553400-128555000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr4:128553400-128555000	Active TSS	Fetal Kidney	kidney
29	chr4:128553400-128555000	Active TSS	Fetal Stomach	stomach
30	chr4:128553400-128555000	Active TSS	Psoas Muscle	Psoas
31	chr4:128553400-128555000	Active TSS	Stomach Smooth Muscle	stomach
32	chr4:128553400-128555000	Active TSS	A549	lung
33	chr4:128553400-128555000	Active TSS	Hela-S3	cervix
34	chr4:128553400-128555000	Active TSS	NHDF-Ad	bronchial
35	chr4:128553400-128555200	Active TSS	H1 Cell Line	embryonic stem cell
36	chr4:128553400-128555200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:128553400-128555200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:128553400-128555200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:128553400-128555200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:128553400-128555200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:128553400-128555200	Active TSS	Brain Hippocampus Middle	brain
42	chr4:128553400-128555200	Active TSS	Duodenum Mucosa	Duodenum
43	chr4:128553400-128555200	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr4:128553400-128555200	Active TSS	Fetal Intestine Large	intestine
45	chr4:128553400-128555200	Active TSS	Ovary	ovary
46	chr4:128553400-128555200	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr4:128553400-128555200	Active TSS	Right Atrium	heart
48	chr4:128553400-128555200	Active TSS	NHLF	lung
49	chr4:128553400-128555600	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr4:128553400-128555600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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