Variant report

Variant	rs4528122
Chromosome Location	chr1:151413790-151413791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151409926..151411809-chr1:151413476..151415968,2	MCF-7	breast:
2	chr1:151412036..151414559-chr1:151416954..151420193,3	MCF-7	breast:
3	1:151411623-151426875..1:151592347-151603110	GM12878	blood:
4	1:151171193-151178589..1:151411623-151426875	GM12878	blood:
5	chr1:151411812..151418574-chr1:151428106..151433466,11	MCF-7	breast:
6	chr1:151411841..151424302-chr1:151427210..151433048,24	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238711	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000206635	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10736380	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs10749662	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204808	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204809	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204811	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204815	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204819	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11204824	0.92[CEU][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs11578888	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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11583968	0.88[EUR][1000 genomes]
rs11584694	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589645	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11801791	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12025432	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12029691	0.88[EUR][1000 genomes]
rs12044242	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12047617	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068166	0.88[EUR][1000 genomes]
rs12068368	0.90[EUR][1000 genomes]
rs12071705	0.90[EUR][1000 genomes]
rs12120726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125310	0.89[EUR][1000 genomes]
rs12740875	0.90[EUR][1000 genomes]
rs12751531	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1342929	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs1887544	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs1887545	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2274533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274535	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2479379	0.88[EUR][1000 genomes]
rs2479385	0.88[EUR][1000 genomes]
rs2495380	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2864122	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118720	0.88[EUR][1000 genomes]
rs34884031	0.89[EUR][1000 genomes]
rs3748550	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs3976737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4246526	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4246527	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs4364884	0.88[EUR][1000 genomes]
rs4603	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs4971040	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4971042	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971043	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4971047	0.92[CEU][hapmap]
rs4971049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61818036	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61818037	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61818039	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587572	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6587573	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587577	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs6587584	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs6587585	0.87[EUR][1000 genomes]
rs6684333	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs6689436	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7542776	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7546151	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs7546933	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv872425	chr1:151325055-151413790	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv1811070	chr1:151403570-151433317	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4528122	POGZ	cis	cerebellum	SCAN
rs4528122	S100A13	cis	cerebellum	SCAN
rs4528122	S100A4	cis	cerebellum	SCAN
rs4528122	SPRR2B	cis	parietal	SCAN
rs4528122	BNIPL	cis	cerebellum	SCAN
rs4528122	SELENBP1	cis	Thyroid	GTEx
rs4528122	SELENBP1	cis	cerebellum	SCAN
rs4528122	MRPS21	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151373400-151416400	Weak transcription	Stomach Mucosa	stomach
2	chr1:151398400-151429600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:151398600-151417400	Weak transcription	Fetal Heart	heart
4	chr1:151400800-151417400	Weak transcription	Aorta	Aorta
5	chr1:151401000-151416200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:151401000-151430000	Weak transcription	Esophagus	oesophagus
7	chr1:151401400-151417400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:151401600-151429200	Weak transcription	Spleen	Spleen
9	chr1:151402200-151416200	Weak transcription	Colonic Mucosa	Colon
10	chr1:151403200-151413800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:151403200-151416800	Weak transcription	HSMMtube	muscle
12	chr1:151403400-151416200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:151405800-151428400	Weak transcription	Right Atrium	heart
14	chr1:151406000-151415800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:151406200-151414800	Strong transcription	Dnd41	blood
16	chr1:151406400-151415200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:151408400-151416200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:151408800-151414600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:151408800-151414600	Strong transcription	Fetal Intestine Large	intestine
20	chr1:151408800-151414800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:151408800-151414800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:151409000-151415000	Strong transcription	Placenta	Placenta
23	chr1:151409200-151414000	Strong transcription	Thymus	Thymus
24	chr1:151409200-151414200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:151409200-151414400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr1:151409200-151415000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr1:151409200-151415200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:151409400-151414800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:151410000-151414600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:151410000-151414800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:151410200-151414600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:151410200-151429800	Weak transcription	Lung	lung
33	chr1:151410800-151414400	Strong transcription	HepG2	liver
34	chr1:151410800-151415800	Strong transcription	Fetal Thymus	thymus
35	chr1:151411000-151414600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:151411200-151414000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:151411200-151414200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:151411200-151414600	Strong transcription	Fetal Brain Female	brain
39	chr1:151411200-151414800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:151411200-151414800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:151411200-151415200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr1:151411400-151414200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:151411400-151414400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr1:151411400-151414400	Weak transcription	Fetal Intestine Small	intestine
45	chr1:151411400-151414600	Strong transcription	Hela-S3	cervix
46	chr1:151411400-151417200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:151411400-151417400	Weak transcription	Gastric	stomach
48	chr1:151411400-151419600	Weak transcription	Fetal Stomach	stomach
49	chr1:151411400-151427200	Weak transcription	Right Ventricle	heart
50	chr1:151411400-151430000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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