Variant report

Variant	rs4949928
Chromosome Location	chr1:85741684-85741685
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	FOXM1	chr1:85741329-85741796	GM12878	blood:	n/a	n/a
2	BRCA1	chr1:85741421-85741879	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:85741401-85742816	HepG2	liver:	n/a	n/a
4	SRF	chr1:85741461-85743025	HCT-116	colon:	n/a	n/a
5	POLR2A	chr1:85741574-85742850	ProgFib	skin:	n/a	n/a
6	TAF1	chr1:85741634-85742811	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr1:85741629-85742189	GM12878	blood:	n/a	n/a
8	STAT1	chr1:85741632-85742729	GM12878	blood:	n/a	n/a
9	RAD21	chr1:85741588-85742394	IMR90	lung:	n/a	chr1:85742287-85742296
10	GABPA	chr1:85741658-85742949	SK-N-SH	brain:	n/a	chr1:85741945-85741954 chr1:85741911-85741918
11	POLR2A	chr1:85740468-85743570	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr1:85740591-85742964	GM12891	blood:	n/a	n/a
13	ZNF143	chr1:85741679-85742630	H1-hESC	embryonic stem cell:	n/a	chr1:85741944-85741954
14	POLR2A	chr1:85741655-85742724	K562	blood:	n/a	n/a
15	PML	chr1:85741383-85741751	GM12878	blood:	n/a	n/a
16	SIN3AK20	chr1:85741227-85742279	PANC-1	pancreas:	n/a	n/a
17	ELF1	chr1:85741515-85742975	HCT-116	colon:	n/a	chr1:85742651-85742662 chr1:85742210-85742219 chr1:85742209-85742222 chr1:85742343-85742355
18	NFIC	chr1:85741649-85742180	ECC-1	luminal epithelium:	n/a	n/a
19	TAF1	chr1:85741434-85742652	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr1:85741665-85742849	NB4	blood:	n/a	chr1:85741944-85741954
21	KAP1	chr1:85740518-85742974	HEK293	kidney:	n/a	chr1:85741050-85741059
22	RELA	chr1:85740582-85742917	GM12878	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
23	POLR2A	chr1:85741210-85742785	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:85741369-85742939	Raji	blood:	n/a	n/a
25	MTA3	chr1:85741236-85742914	GM12878	blood:	n/a	n/a
26	HEY1	chr1:85741619-85742871	HepG2	liver:	n/a	chr1:85741928-85741943 chr1:85742088-85742103 chr1:85742080-85742095
27	MYC	chr1:85741486-85742880	NB4	blood:	n/a	chr1:85741944-85741954
28	ELK4	chr1:85741271-85742801	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr1:85740603-85742874	K562	blood:	n/a	n/a
30	POU2F2	chr1:85741323-85741849	GM12891	blood:	n/a	chr1:85741534-85741542 chr1:85741534-85741544
31	POLR2A	chr1:85741287-85742805	GM12891	blood:	n/a	n/a
32	CREB1	chr1:85741595-85742788	K562	blood:	n/a	n/a
33	CHD1	chr1:85740696-85742142	GM12878	blood:	n/a	n/a
34	HCFC1	chr1:85740700-85743065	Hela-S3	cervix:	n/a	n/a
35	SPI1	chr1:85741670-85742802	HL-60	blood:	n/a	chr1:85741908-85741921
36	POLR2A	chr1:85741682-85742910	U87	brain:	n/a	n/a
37	MTA3	chr1:85741241-85742169	GM12878	blood:	n/a	n/a
38	RELA	chr1:85740690-85742803	GM19099	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
39	POLR2A	chr1:85740638-85742911	GM12878	blood:	n/a	n/a
40	RELA	chr1:85740946-85741847	GM10847	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
41	POLR2A	chr1:85741656-85742806	MCF-7	breast:	n/a	n/a
42	POLR2A	chr1:85741248-85742904	GM18505	blood:	n/a	n/a
43	MAFK	chr1:85741574-85742342	K562	blood:	n/a	n/a
44	POLR2A	chr1:85740399-85742970	HUVEC	blood vessel:	n/a	n/a
45	GABPA	chr1:85741656-85742832	MCF-7	breast:	n/a	chr1:85741945-85741954 chr1:85741911-85741918
46	RELA	chr1:85741268-85742847	GM15510	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
47	SIN3AK20	chr1:85741393-85742850	PANC-1	pancreas:	n/a	n/a
48	POLR2A	chr1:85741380-85742868	GM19193	blood:	n/a	n/a
49	SIN3AK20	chr1:85741430-85742376	K562	blood:	n/a	n/a
50	BCLAF1	chr1:85741358-85742401	GM12878	blood:	n/a	chr1:85741485-85741494 chr1:85742083-85742092 chr1:85742210-85742219

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:85741649-85741699	HAEpiC	amniotic membrane:	n/a
2	chr1:85741649-85741699	BE2_C	brain:	n/a
3	chr1:85741649-85741699	HCM	heart:	n/a
4	chr1:85741649-85741699	AG04449	skin:	fetal
5	chr1:85741649-85741699	ovcar-3	ovarian:	n/a
6	chr1:85741649-85741699	Jurkat	blood:	n/a
7	chr1:85741649-85741699	MCF10A-Er-Src	breast:	n/a
8	chr1:85741649-85741699	PFSK-1	brain:	n/a
9	chr1:85741649-85741699	GM12891	blood:	n/a
10	chr1:85741649-85741699	ProgFib	skin:	n/a
11	chr1:85741649-85741699	GM19239	blood:	n/a
12	chr1:85741649-85741699	HEK293	kidney:	embryo
13	chr1:85741649-85741699	PANC-1	pancreas:	n/a
14	chr1:85741649-85741699	SK-N-SH_RA	brain:	n/a
15	chr1:85741649-85741699	HepG2	liver:	n/a
16	chr1:85741649-85741699	RPTEC	kidney:	n/a
17	chr1:85741649-85741699	SAEC	small airway:	n/a
18	chr1:85741649-85741699	GM06990	blood:	n/a
19	chr1:85741649-85741699	HMEC	breast:	n/a
20	chr1:85741649-85741699	PrEC	prostate:	n/a
21	chr1:85741649-85741699	HCPEpiC	choroid plexus:	n/a
22	chr1:85741649-85741699	NHDF-neo	bronchial:	n/a
23	chr1:85741649-85741699	HNPCEpiC	eye:	n/a
24	chr1:85741649-85741699	Caco-2	colon:	n/a
25	chr1:85741649-85741699	HCT-116	colon:	n/a
26	chr1:85741649-85741699	AG09309	skin:	n/a
27	chr1:85741649-85741699	AoSMC	blood vessel:	n/a
28	chr1:85741649-85741699	CMK	blood:	n/a
29	chr1:85741649-85741699	A549	lung:	n/a
30	chr1:85741649-85741699	SK-N-SH	brain:	n/a
31	chr1:85741649-85741699	K562	blood:	n/a
32	chr1:85741649-85741699	HPAEpiC	pulmonary alveolar:	n/a
33	chr1:85741649-85741699	ECC-1	luminal epithelium:	n/a
34	chr1:85741649-85741699	SKMC	muscle:	n/a
35	chr1:85741649-85741699	Hepatocyte	liver:	n/a
36	chr1:85741649-85741699	HRCEpiC	kidney:	n/a
37	chr1:85741649-85741699	HEEpiC	esophagus:	n/a
38	chr1:85741649-85741699	NT2-D1	testis:	n/a
39	chr1:85741649-85741699	AG10803	skin:	n/a
40	chr1:85741649-85741699	HL-60	blood:	n/a
41	chr1:85741649-85741699	HRPEpiC	eye:	n/a
42	chr1:85741649-85741699	NB4	blood:	n/a
43	chr1:85741649-85741699	H1-hESC	embryonic stem cell:	embryo
44	chr1:85741649-85741699	MCF-7	breast:	n/a
45	chr1:85741649-85741699	HCF	heart:	n/a
46	chr1:85741649-85741699	GM12878	blood:	n/a
47	chr1:85741649-85741699	Hela-S3	cervix:	n/a
48	chr1:85741649-85741699	GM12892	blood:	n/a
49	chr1:85741649-85741699	AG09319	gingival:	n/a
50	chr1:85741649-85741699	HRE	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85739753..85743262-chr1:86045535..86049012,3	K562	blood:
2	chr1:85665913..85668656-chr1:85741362..85743092,3	MCF-7	breast:
3	chr1:85665631..85669772-chr1:85739485..85744059,5	K562	blood:
4	chr1:85740297..85741951-chr1:85930278..85931798,2	MCF-7	breast:
5	chr1:85740856..85742558-chr1:86046586..86048600,2	MCF-7	breast:
6	chr1:85722628..85726570-chr1:85740869..85744448,4	MCF-7	breast:
7	chr1:85723214..85729954-chr1:85738689..85743771,11	K562	blood:
8	chr1:85665227..85667257-chr1:85740935..85743875,2	K562	blood:
9	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

Variant related genes	Relation type
ENSG00000223653	TF binding region
ENSG00000223653	CpG island
ENSG00000153904	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000162642	Chromatin interaction
ENSG00000097096	Chromatin interaction
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10747317	0.90[CHB][hapmap]
rs10782542	0.80[CHB][hapmap]
rs10782543	0.90[CHB][hapmap]
rs11161573	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161585	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11161586	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11161588	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11161592	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11555520	0.88[CEU][hapmap]
rs11576939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580090	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11583827	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs11587512	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11590047	0.85[ASN][1000 genomes]
rs12061512	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12084253	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12093484	1.00[CHB][hapmap]
rs12403960	0.85[ASN][1000 genomes]
rs12405767	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12754032	0.85[ASN][1000 genomes]
rs17125445	1.00[CHB][hapmap]
rs2647394	0.88[CEU][hapmap]
rs34743622	0.85[ASN][1000 genomes]
rs4949927	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55808228	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57483398	0.82[ASN][1000 genomes]
rs60325409	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668948	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6670921	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7554249	1.00[CHB][hapmap]
rs9432848	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85739200-85743000	Active TSS	Psoas Muscle	Psoas
2	chr1:85739600-85741800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr1:85739600-85742200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:85739800-85741800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:85739800-85742800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:85740000-85741800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr1:85740200-85741800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr1:85740200-85743200	Active TSS	Colonic Mucosa	Colon
9	chr1:85740400-85741800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr1:85740400-85742400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:85740400-85742600	Active TSS	GM12878-XiMat	blood
12	chr1:85740400-85742800	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr1:85740600-85741800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:85740600-85741800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr1:85740600-85741800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr1:85740600-85741800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:85740600-85741800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:85740600-85741800	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr1:85740600-85741800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:85740600-85742000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr1:85740600-85742800	Active TSS	Fetal Intestine Large	intestine
22	chr1:85740600-85742800	Active TSS	Ovary	ovary
23	chr1:85740600-85743000	Active TSS	Right Atrium	heart
24	chr1:85740600-85743000	Active TSS	Right Ventricle	heart
25	chr1:85740600-85743200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr1:85740600-85743200	Active TSS	Esophagus	oesophagus
27	chr1:85740800-85741800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr1:85740800-85741800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr1:85740800-85741800	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr1:85740800-85741800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr1:85740800-85741800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:85740800-85741800	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr1:85740800-85742200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:85740800-85742600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:85740800-85742600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr1:85740800-85742600	Active TSS	HMEC	breast
37	chr1:85740800-85742600	Active TSS	NHEK	skin
38	chr1:85740800-85742800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:85740800-85742800	Active TSS	Left Ventricle	heart
40	chr1:85740800-85742800	Active TSS	Stomach Mucosa	stomach
41	chr1:85740800-85742800	Active TSS	NHDF-Ad	bronchial
42	chr1:85740800-85742800	Active TSS	NHLF	lung
43	chr1:85740800-85743000	Active TSS	Aorta	Aorta
44	chr1:85740800-85743400	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:85741000-85741800	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr1:85741000-85741800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr1:85741000-85741800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr1:85741000-85742600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr1:85741000-85742600	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr1:85741000-85742600	Active TSS	NH-A	brain

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