Variant report

Variant	rs72649970
Chromosome Location	chr1:210406599-210406600
allele	A/C
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	E2F4	chr1:210406462-210406781	MCF10A-Er-Src	breast:	n/a	chr1:210406562-210406577 chr1:210406620-210406632 chr1:210406572-210406581
2	MAX	chr1:210406390-210407519	SK-N-SH	brain:	n/a	chr1:210406540-210406549
3	SMARCC1	chr1:210406586-210407990	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr1:210406480-210406630	SK-N-SH_RA	brain:	n/a	n/a
5	MAX	chr1:210406455-210407697	SK-N-SH	brain:	n/a	chr1:210406540-210406549
6	ZBTB7A	chr1:210406439-210406890	ECC-1	luminal epithelium:	n/a	n/a
7	MAZ	chr1:210405793-210408090	IMR90	lung:	n/a	chr1:210406540-210406549
8	EGR1	chr1:210406590-210407390	HCT-116	colon:	n/a	chr1:210406906-210406919 chr1:210406948-210406962 chr1:210406906-210406919 chr1:210406900-210406913 chr1:210406906-210406919 chr1:210406906-210406919 chr1:210406907-210406918 chr1:210406901-210406923 chr1:210406907-210406917 chr1:210406905-210406920 chr1:210406631-210406641 chr1:210406907-210406917 chr1:210406903-210406917 chr1:210406905-210406919 chr1:210406895-210406905 chr1:210406907-210406916 chr1:210406906-210406916
9	EGR1	chr1:210406289-210406613	ECC-1	luminal epithelium:	n/a	chr1:210406569-210406579 chr1:210406332-210406342 chr1:210406564-210406577
10	TEAD4	chr1:210406377-210407655	SK-N-SH	brain:	n/a	n/a
11	MYC	chr1:210406528-210406668	MCF-7	breast:	n/a	chr1:210406540-210406549
12	POLR2A	chr1:210405595-210408558	H1-neurons	neurons:	n/a	n/a
13	EGR1	chr1:210406525-210407936	HCT-116	colon:	n/a	chr1:210406906-210406919 chr1:210406948-210406962 chr1:210406906-210406919 chr1:210406569-210406579 chr1:210407621-210407636 chr1:210407621-210407635 chr1:210406900-210406913 chr1:210406906-210406919 chr1:210406906-210406919 chr1:210406907-210406918 chr1:210406901-210406923 chr1:210407623-210407633 chr1:210406907-210406917 chr1:210406905-210406920 chr1:210406631-210406641 chr1:210406907-210406917 chr1:210406903-210406917 chr1:210407623-210407632 chr1:210406905-210406919 chr1:210406895-210406905 chr1:210407622-210407635 chr1:210406907-210406916 chr1:210407623-210407634 chr1:210407622-210407635 chr1:210407622-210407635 chr1:210406906-210406916 chr1:210407622-210407635 chr1:210407617-210407639 chr1:210406564-210406577
14	HA-E2F1	chr1:210405555-210407854	MCF-7	breast:	n/a	chr1:210405557-210405566 chr1:210406562-210406577 chr1:210405978-210405988 chr1:210405975-210405985 chr1:210406950-210406960 chr1:210406620-210406632 chr1:210407579-210407589 chr1:210406572-210406581
15	TCF7L2	chr1:210406552-210407801	HCT-116	colon:	n/a	chr1:210407431-210407441
16	CTBP2	chr1:210405979-210407958	H1-hESC	embryonic stem cell:	n/a	n/a
17	E2F6	chr1:210406420-210407363	A549	lung:	n/a	chr1:210406562-210406577 chr1:210406950-210406960 chr1:210406620-210406632 chr1:210406572-210406581
18	TAF1	chr1:210406429-210407449	H1-neurons	neurons:	n/a	n/a
19	MAX	chr1:210406398-210407574	A549	lung:	n/a	chr1:210406540-210406549
20	MAX	chr1:210406319-210407751	A549	lung:	n/a	chr1:210406540-210406549
21	SMARCB1	chr1:210406546-210407922	Hela-S3	cervix:	n/a	n/a
22	REST	chr1:210405235-210408055	H1-neurons	neurons:	n/a	n/a
23	EGR1	chr1:210406202-210407163	K562	blood:	n/a	chr1:210406906-210406919 chr1:210406948-210406962 chr1:210406906-210406919 chr1:210406569-210406579 chr1:210406332-210406342 chr1:210406900-210406913 chr1:210406906-210406919 chr1:210406906-210406919 chr1:210406907-210406918 chr1:210406901-210406923 chr1:210406907-210406917 chr1:210406905-210406920 chr1:210406631-210406641 chr1:210406907-210406917 chr1:210406903-210406917 chr1:210406905-210406919 chr1:210406895-210406905 chr1:210406907-210406916 chr1:210406906-210406916 chr1:210406564-210406577
24	POLR2A	chr1:210405931-210407316	MCF-7	breast:	n/a	n/a
25	POLR2A	chr1:210405721-210407760	HUVEC	blood vessel:	n/a	n/a
26	BACH1	chr1:210405970-210407150	H1-hESC	embryonic stem cell:	n/a	n/a
27	SIN3A	chr1:210406525-210408381	H1-hESC	embryonic stem cell:	n/a	chr1:210407705-210407714 chr1:210407487-210407496 chr1:210407512-210407523
28	REST	chr1:210406484-210407429	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr1:210406073-210406840	HUVEC	blood vessel:	n/a	n/a
30	EP300	chr1:210406419-210407787	SK-N-SH	brain:	n/a	chr1:210406943-210406959 chr1:210406861-210406870 chr1:210406946-210406955 chr1:210406944-210406960 chr1:210406951-210406960 chr1:210407457-210407467
31	POLR2A	chr1:210406426-210407329	H1-neurons	neurons:	n/a	n/a
32	E2F6	chr1:210406511-210406641	K562	blood:	n/a	chr1:210406562-210406577 chr1:210406620-210406632 chr1:210406572-210406581
33	ZNF263	chr1:210406554-210408050	HEK293-T-REx	kidney:	n/a	chr1:210407035-210407056 chr1:210406919-210406928
34	TCF12	chr1:210405200-210408026	SK-N-SH	brain:	n/a	chr1:210407710-210407720

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:210406599-210406649	Hepatocyte	liver:	n/a
2	chr1:210406599-210406649	AoSMC	blood vessel:	n/a
3	chr1:210406599-210406649	AG09309	skin:	n/a
4	chr1:210406599-210406649	HEEpiC	esophagus:	n/a
5	chr1:210406599-210406649	NH-A	brain:	n/a
6	chr1:210406599-210406649	AG04450	lung:	fetal
7	chr1:210406599-210406649	GM12878	blood:	n/a
8	chr1:210406599-210406649	RPTEC	kidney:	n/a
9	chr1:210406599-210406649	T-47D	breast:	n/a
10	chr1:210406599-210406649	PANC-1	pancreas:	n/a
11	chr1:210406599-210406649	BE2_C	brain:	n/a
12	chr1:210406599-210406649	LNCaP	prostate:	n/a
13	chr1:210406599-210406649	HCPEpiC	choroid plexus:	n/a
14	chr1:210406599-210406649	AG09319	gingival:	n/a
15	chr1:210406599-210406649	Jurkat	blood:	n/a
16	chr1:210406599-210406649	GM12891	blood:	n/a
17	chr1:210406599-210406649	HAEpiC	amniotic membrane:	n/a
18	chr1:210406599-210406649	NT2-D1	testis:	n/a
19	chr1:210406599-210406649	HRCEpiC	kidney:	n/a
20	chr1:210406599-210406649	SK-N-SH_RA	brain:	n/a
21	chr1:210406599-210406649	NHDF-neo	bronchial:	n/a
22	chr1:210406599-210406649	HIPEpiC	eye:	n/a
23	chr1:210406599-210406649	GM12892	blood:	n/a
24	chr1:210406599-210406649	SAEC	small airway:	n/a
25	chr1:210406599-210406649	HPAEpiC	pulmonary alveolar:	n/a
26	chr1:210406599-210406649	PrEC	prostate:	n/a
27	chr1:210406599-210406649	SKMC	muscle:	n/a
28	chr1:210406599-210406649	GM19239	blood:	n/a
29	chr1:210406599-210406649	K562	blood:	n/a
30	chr1:210406599-210406649	HCM	heart:	n/a
31	chr1:210406599-210406649	ovcar-3	ovarian:	n/a
32	chr1:210406599-210406649	AG04449	skin:	fetal
33	chr1:210406599-210406649	HCF	heart:	n/a
34	chr1:210406599-210406649	Caco-2	colon:	n/a
35	chr1:210406599-210406649	HEK293	kidney:	embryo
36	chr1:210406599-210406649	IMR90	lung:	fetal
37	chr1:210406599-210406649	BJ	skin:	n/a
38	chr1:210406599-210406649	PFSK-1	brain:	n/a
39	chr1:210406599-210406649	U87	brain:	n/a
40	chr1:210406599-210406649	HNPCEpiC	eye:	n/a
41	chr1:210406599-210406649	HMEC	breast:	n/a
42	chr1:210406599-210406649	HL-60	blood:	n/a
43	chr1:210406599-210406649	HUVEC	blood vessel:	n/a
44	chr1:210406599-210406649	HepG2	liver:	n/a
45	chr1:210406599-210406649	SK-N-MC	brain:	n/a
46	chr1:210406599-210406649	GM06990	blood:	n/a
47	chr1:210406599-210406649	MCF-7	breast:	n/a
48	chr1:210406599-210406649	Hela-S3	cervix:	n/a
49	chr1:210406599-210406649	CMK	blood:	n/a
50	chr1:210406599-210406649	SK-N-SH	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:210405800..210407964-chr1:210502205..210503882,2	MCF-7	breast:
2	chr1:210404317..210408653-chr1:210545033..210548956,7	MCF-7	breast:
3	chr1:210404553..210406882-chr6:30538400..30541136,2	MCF-7	breast:
4	chr1:210405867..210408909-chr1:210535692..210538632,3	MCF-7	breast:
5	chr1:210406407..210409749-chr1:210545963..210547821,3	MCF-7	breast:

Variant related genes	Relation type
SERTAD4-AS1	TF binding region
SERTAD4	TF binding region
SERTAD4	CpG island
SERTAD4-AS1	CpG island
ENSG00000204574	Chromatin interaction
ENSG00000054392	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12561877	1.00[AMR][1000 genomes]
rs12562421	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12565234	1.00[AMR][1000 genomes]
rs12567185	1.00[AMR][1000 genomes]
rs4144930	1.00[AMR][1000 genomes]
rs72649936	1.00[AMR][1000 genomes]
rs72649939	1.00[AMR][1000 genomes]
rs72649941	1.00[AMR][1000 genomes]
rs72649942	1.00[AMR][1000 genomes]
rs72649943	1.00[AMR][1000 genomes]
rs72649944	1.00[AMR][1000 genomes]
rs72649945	1.00[AMR][1000 genomes]
rs72649946	1.00[AMR][1000 genomes]
rs72649947	1.00[AMR][1000 genomes]
rs72649950	1.00[AMR][1000 genomes]
rs72649951	1.00[AMR][1000 genomes]
rs72649953	1.00[AMR][1000 genomes]
rs72649954	1.00[AMR][1000 genomes]
rs72649958	1.00[AMR][1000 genomes]
rs72649961	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72649963	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72649965	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72649971	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649972	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649974	1.00[AMR][1000 genomes];0.87[EUR][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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv3422029	chr1:210404854-210407702	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3334541	chr1:210405229-210407377	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210405000-210407400	Active TSS	Stomach Smooth Muscle	stomach
2	chr1:210405000-210407600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:210405200-210406600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:210405200-210407600	Active TSS	NH-A	brain
5	chr1:210405400-210406600	Active TSS	Muscle Satellite Cultured Cells	--
6	chr1:210405400-210407600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:210405400-210407600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:210405400-210407600	Active TSS	Right Ventricle	heart
9	chr1:210405400-210407800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:210405400-210407800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:210405400-210407800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:210405400-210407800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr1:210405400-210407800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr1:210405400-210407800	Active TSS	Colon Smooth Muscle	Colon
15	chr1:210405400-210407800	Active TSS	Rectal Smooth Muscle	rectum
16	chr1:210405400-210408000	Bivalent Enhancer	Fetal Brain Male	brain
17	chr1:210405400-210408000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:210405600-210406600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:210405600-210406600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:210405600-210406600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:210405600-210406600	Bivalent Enhancer	Primary T cells from cord blood	blood
22	chr1:210405600-210406600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr1:210405600-210406600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
24	chr1:210405600-210406600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:210405600-210406600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
26	chr1:210405600-210406600	Active TSS	HMEC	breast
27	chr1:210405600-210406600	Bivalent/Poised TSS	Osteobl	bone
28	chr1:210405600-210406800	Flanking Bivalent TSS/Enh	Thymus	Thymus
29	chr1:210405600-210407000	Active TSS	Colonic Mucosa	Colon
30	chr1:210405600-210407000	Bivalent Enhancer	Fetal Lung	lung
31	chr1:210405600-210407000	Active TSS	Right Atrium	heart
32	chr1:210405600-210407400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:210405600-210407400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:210405600-210407400	Active TSS	HSMM	muscle
35	chr1:210405600-210407600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr1:210405600-210407600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:210405600-210407600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:210405600-210407600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:210405600-210407600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:210405600-210407600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
41	chr1:210405600-210407600	Active TSS	Brain Cingulate Gyrus	brain
42	chr1:210405600-210407600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr1:210405600-210407600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
44	chr1:210405600-210407600	Active TSS	Left Ventricle	heart
45	chr1:210405600-210407600	Active TSS	Ovary	ovary
46	chr1:210405600-210407600	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr1:210405600-210407600	Bivalent/Poised TSS	A549	lung
48	chr1:210405600-210407600	Active TSS	HSMMtube	muscle
49	chr1:210405600-210407600	Active TSS	NHLF	lung
50	chr1:210405600-210407800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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