Variant report

Variant	rs7528979
Chromosome Location	chr1:10093457-10093458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10092839-10093578	U87	brain:	n/a	n/a
2	POLR2A	chr1:10092956-10093801	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAZ	chr1:10092447-10093952	K562	blood:	n/a	chr1:10093004-10093017 chr1:10093001-10093020 chr1:10093006-10093015 chr1:10093007-10093016 chr1:10093004-10093017 chr1:10093004-10093017 chr1:10093005-10093016 chr1:10092822-10092831 chr1:10093006-10093015
4	GTF2F1	chr1:10092459-10093961	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:10092855-10093576	MCF-7	breast:	n/a	n/a
6	POLR2A	chr1:10092893-10093521	H1-hESC	embryonic stem cell:	n/a	n/a
7	YY1	chr1:10092305-10093785	SK-N-SH	brain:	n/a	chr1:10093018-10093035 chr1:10093025-10093033 chr1:10092794-10092808 chr1:10092791-10092805 chr1:10092835-10092846 chr1:10092800-10092811 chr1:10092600-10092609 chr1:10093024-10093034 chr1:10092795-10092809 chr1:10093012-10093034 chr1:10092878-10092889 chr1:10093023-10093031
8	RCOR1	chr1:10092406-10093971	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:10092703-10093586	HUVEC	blood vessel:	n/a	n/a
10	TCF7L2	chr1:10092493-10093885	Hela-S3	cervix:	n/a	n/a
11	RAD21	chr1:10092245-10094157	SK-N-SH	brain:	n/a	n/a
12	SIN3AK20	chr1:10092967-10093963	H1-hESC	embryonic stem cell:	n/a	n/a
13	JUND	chr1:10092462-10093704	K562	blood:	n/a	chr1:10092988-10092997
14	POLR2A	chr1:10092805-10093538	SK-N-SH	brain:	n/a	n/a
15	IRF1	chr1:10092415-10094093	K562	blood:	n/a	chr1:10093173-10093187 chr1:10092572-10092592 chr1:10093168-10093182 chr1:10092983-10092997 chr1:10092902-10092916 chr1:10092572-10092585 chr1:10092577-10092591
16	CHD1	chr1:10093012-10094412	H1-hESC	embryonic stem cell:	n/a	chr1:10093063-10093073 chr1:10093141-10093151
17	NR2F2	chr1:10092243-10094003	K562	blood:	n/a	n/a
18	ELF1	chr1:10092470-10093573	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:10092392-10093928	H1-neurons	neurons:	n/a	n/a
20	MAX	chr1:10092453-10094091	Hela-S3	cervix:	n/a	chr1:10093004-10093017 chr1:10093001-10093020 chr1:10093006-10093015 chr1:10093007-10093016 chr1:10093004-10093017 chr1:10093004-10093017 chr1:10093005-10093016 chr1:10092822-10092831 chr1:10093006-10093015
21	MAZ	chr1:10092270-10094033	IMR90	lung:	n/a	chr1:10093004-10093017 chr1:10093001-10093020 chr1:10093006-10093015 chr1:10093007-10093016 chr1:10093004-10093017 chr1:10093004-10093017 chr1:10093005-10093016 chr1:10092822-10092831 chr1:10093006-10093015
22	EP300	chr1:10092540-10094968	K562	blood:	n/a	chr1:10094798-10094808 chr1:10092873-10092889 chr1:10094604-10094618 chr1:10092796-10092805
23	POLR2A	chr1:10092830-10093575	HL-60	blood:	n/a	n/a
24	MAFK	chr1:10092411-10094018	Hela-S3	cervix:	n/a	n/a
25	SIN3AK20	chr1:10092916-10093730	SK-N-SH	brain:	n/a	n/a
26	PML	chr1:10092570-10094057	K562	blood:	n/a	n/a
27	POLR2A	chr1:10092160-10093931	K562	blood:	n/a	n/a
28	MXI1	chr1:10092556-10093737	GM12878	blood:	n/a	chr1:10092818-10092833 chr1:10093005-10093014 chr1:10092816-10092831
29	MXI1	chr1:10092489-10093482	HepG2	liver:	n/a	chr1:10092818-10092833 chr1:10093005-10093014 chr1:10092816-10092831
30	MYC	chr1:10092530-10093872	NB4	blood:	n/a	chr1:10093004-10093017 chr1:10093001-10093020 chr1:10093006-10093015 chr1:10093007-10093016 chr1:10093004-10093017 chr1:10093004-10093017 chr1:10093005-10093016 chr1:10092822-10092831 chr1:10093006-10093015
31	KAP1	chr1:10092423-10093811	U2OS	brain:	n/a	n/a
32	TAF1	chr1:10092546-10093482	HepG2	liver:	n/a	n/a
33	SIN3A	chr1:10092459-10093988	H1-hESC	embryonic stem cell:	n/a	chr1:10093005-10093014 chr1:10092835-10092846 chr1:10092878-10092889 chr1:10092833-10092846 chr1:10093007-10093016
34	POLR2A	chr1:10092471-10093810	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:10092911-10093550	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:10092817-10093559	GM12878	blood:	n/a	n/a
37	HA-E2F1	chr1:10092307-10093905	MCF-7	breast:	n/a	chr1:10092796-10092805 chr1:10092600-10092609 chr1:10093169-10093178 chr1:10092987-10092996 chr1:10092903-10092912
38	TAF1	chr1:10092863-10093576	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr1:10092453-10093974	GM12891	blood:	n/a	n/a
40	SMARCC1	chr1:10092505-10093949	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr1:10092467-10093514	HCT-116	colon:	n/a	n/a
42	PML	chr1:10092957-10093956	K562	blood:	n/a	n/a
43	RAD21	chr1:10092451-10093535	SK-N-SH_RA	brain:	n/a	n/a
44	TAL1	chr1:10092637-10093497	K562	blood:	n/a	n/a
45	CHD2	chr1:10092566-10093699	GM12878	blood:	n/a	chr1:10093063-10093073 chr1:10093141-10093151
46	YY1	chr1:10092536-10093560	SK-N-SH	brain:	n/a	chr1:10093018-10093035 chr1:10093025-10093033 chr1:10092794-10092808 chr1:10092791-10092805 chr1:10092835-10092846 chr1:10092800-10092811 chr1:10092600-10092609 chr1:10093024-10093034 chr1:10092795-10092809 chr1:10093012-10093034 chr1:10092878-10092889 chr1:10093023-10093031
47	POLR2A	chr1:10092454-10093600	ECC-1	luminal epithelium:	n/a	n/a
48	NRF1	chr1:10092634-10093583	GM12878	blood:	n/a	chr1:10092796-10092805 chr1:10092944-10092955 chr1:10092877-10092888
49	POLR2A	chr1:10092455-10093950	K562	blood:	n/a	n/a
50	YY1	chr1:10092549-10093774	H1-hESC	embryonic stem cell:	n/a	chr1:10093018-10093035 chr1:10093025-10093033 chr1:10092794-10092808 chr1:10092791-10092805 chr1:10092835-10092846 chr1:10092800-10092811 chr1:10092600-10092609 chr1:10093024-10093034 chr1:10092795-10092809 chr1:10093012-10093034 chr1:10092878-10092889 chr1:10093023-10093031

No.	Distal block	Cell Line	Cell type
1	chr1:10002061..10004916-chr1:10091716..10094596,6	MCF-7	breast:
2	chr1:9969329..9971047-chr1:10093028..10095066,2	K562	blood:
3	chr1:10002125..10006916-chr1:10090169..10095056,10	K562	blood:
4	chr1:10001502..10006445-chr1:10090966..10096976,9	MCF-7	breast:
5	chr1:10001294..10005828-chr1:10093316..10096471,4	K562	blood:
6	chr1:10092960..10093589-chr2:9770583..9771175,2	Hela-S3	cervix:
7	chr1:9929452..9932865-chr1:10092666..10095157,3	K562	blood:
8	chr1:9968980..9971143-chr1:10091275..10094032,2	MCF-7	breast:

Variant related genes	Relation type
UBE4B	TF binding region
ENSG00000134308	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000178585	Chromatin interaction
ENSG00000173614	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1220421	0.84[CHD][hapmap]
rs1234694	0.84[CHD][hapmap];0.92[LWK][hapmap];0.90[MKK][hapmap]
rs2890358	0.81[ASW][hapmap];0.86[CHD][hapmap];0.92[LWK][hapmap];0.88[MKK][hapmap]
rs3003376	0.87[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3003378	0.93[ASW][hapmap];0.93[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs3013788	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3123522	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3762290	0.93[ASW][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs58528460	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61650275	0.80[EUR][1000 genomes]
rs6541073	0.83[CHD][hapmap]
rs6541075	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6664631	0.90[JPT][hapmap]
rs6671289	0.93[ASW][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs6676280	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6693449	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6696978	1.00[YRI][hapmap]
rs7517806	0.80[ASN][1000 genomes]
rs7517812	0.81[ASW][hapmap];0.85[CEU][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs7539725	0.85[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs9919194	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7528979	LZIC	cis	lymphoblastoid	seeQTL
rs7528979	KIF1B	cis	parietal	SCAN
rs7528979	LZIC	cis	multi-tissue	Pritchard
rs7528979	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs7528979	LZIC	cis	Lymphoblastoid	GTEx
rs7528979	UBE4B	cis	Liver	GTEx
rs7528979	HES3	cis	cerebellum	SCAN
rs7528979	MTHFR	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10091600-10094400	Active TSS	A549	lung
2	chr1:10092200-10093600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:10092200-10094000	Active TSS	Fetal Lung	lung
4	chr1:10092200-10094200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:10092200-10094200	Active TSS	Rectal Smooth Muscle	rectum
6	chr1:10092200-10094600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:10092200-10094600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:10092200-10094800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:10092200-10094800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:10092200-10095600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:10092200-10096200	Active TSS	K562	blood
12	chr1:10092400-10093600	Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr1:10092400-10093600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr1:10092400-10093800	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr1:10092400-10093800	Active TSS	Brain Anterior Caudate	brain
16	chr1:10092400-10093800	Active TSS	Brain Hippocampus Middle	brain
17	chr1:10092400-10094000	Active TSS	Brain Substantia Nigra	brain
18	chr1:10092400-10094000	Active TSS	Duodenum Mucosa	Duodenum
19	chr1:10092400-10094000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:10092400-10094000	Active TSS	Pancreas	Pancrea
21	chr1:10092400-10094000	Active TSS	Stomach Mucosa	stomach
22	chr1:10092400-10094000	Bivalent/Poised TSS	HepG2	liver
23	chr1:10092400-10094200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr1:10092400-10094200	Active TSS	Fetal Muscle Trunk	muscle
25	chr1:10092400-10094400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:10092400-10094400	Active TSS	Brain Angular Gyrus	brain
27	chr1:10092400-10094400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr1:10092400-10094600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:10092400-10094600	Active TSS	Colonic Mucosa	Colon
30	chr1:10092400-10094600	Active TSS	Fetal Brain Female	brain
31	chr1:10092400-10094600	Active TSS	Fetal Intestine Large	intestine
32	chr1:10092400-10094600	Active TSS	Thymus	Thymus
33	chr1:10092400-10094600	Active TSS	NHDF-Ad	bronchial
34	chr1:10092400-10094800	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr1:10092400-10094800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:10092400-10094800	Active TSS	Fetal Kidney	kidney
37	chr1:10092400-10094800	Active TSS	Psoas Muscle	Psoas
38	chr1:10092400-10094800	Active TSS	Right Ventricle	heart
39	chr1:10092400-10095000	Active TSS	H1 Cell Line	embryonic stem cell
40	chr1:10092400-10095000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr1:10092400-10095000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:10092400-10095000	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr1:10092400-10095000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:10092400-10095000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:10092400-10095000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:10092400-10095000	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr1:10092400-10095000	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr1:10092400-10095000	Active TSS	Left Ventricle	heart
49	chr1:10092400-10095000	Active TSS	Ovary	ovary
50	chr1:10092400-10095000	Active TSS	Right Atrium	heart

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