Variant report

Variant	rs624706
Chromosome Location	chr1:210407031-210407032
allele	G/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	RXRA	chr1:210406681-210407562	SK-N-SH	brain:	n/a	n/a
2	EGR1	chr1:210406687-210407160	ECC-1	luminal epithelium:	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 chr1:210406907-210406917 chr1:210406903-210406917 chr1:210406905-210406919 chr1:210406895-210406905 chr1:210406907-210406916 chr1:210406906-210406916
3	SIN3AK20	chr1:210406692-210407721	SK-N-SH	brain:	n/a	n/a
4	MAX	chr1:210406390-210407519	SK-N-SH	brain:	n/a	chr1:210406540-210406549
5	JUND	chr1:210407026-210407653	H1-hESC	embryonic stem cell:	n/a	chr1:210407582-210407591
6	EP300	chr1:210407023-210407418	SK-N-SH_RA	brain:	n/a	n/a
7	SMARCC1	chr1:210406586-210407990	Hela-S3	cervix:	n/a	n/a
8	TCF12	chr1:210406973-210407570	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr1:210406865-210407551	HUVEC	blood vessel:	n/a	n/a
10	MAX	chr1:210406455-210407697	SK-N-SH	brain:	n/a	chr1:210406540-210406549
11	TCF7L2	chr1:210406960-210407876	Hela-S3	cervix:	n/a	chr1:210407431-210407441
12	POLR2A	chr1:210406990-210407239	Gliobla	brain:	n/a	n/a
13	TCF12	chr1:210406741-210407842	SK-N-SH	brain:	n/a	chr1:210407710-210407720
14	UBTF	chr1:210406885-210407354	K562	blood:	n/a	n/a
15	EP300	chr1:210406870-210407742	ECC-1	luminal epithelium:	n/a	chr1:210406943-210406959 chr1:210406946-210406955 chr1:210406944-210406960 chr1:210406951-210406960 chr1:210407457-210407467
16	FOXA1	chr1:210406958-210407810	T-47D	breast:	n/a	chr1:210407454-210407466
17	EGR1	chr1:210406729-210407062	H1-hESC	embryonic stem cell:	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 chr1:210406907-210406917 chr1:210406903-210406917 chr1:210406905-210406919 chr1:210406895-210406905 chr1:210406907-210406916 chr1:210406906-210406916
18	FOSL2	chr1:210406952-210407691	SK-N-SH	brain:	n/a	chr1:210407582-210407591
19	MAZ	chr1:210405793-210408090	IMR90	lung:	n/a	chr1:210406540-210406549
20	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
21	TCF12	chr1:210406815-210407525	ECC-1	luminal epithelium:	n/a	n/a
22	TEAD4	chr1:210406377-210407655	SK-N-SH	brain:	n/a	n/a
23	PBX3	chr1:210407016-210407607	SK-N-SH	brain:	n/a	n/a
24	MAX	chr1:210406791-210407335	ECC-1	luminal epithelium:	n/a	n/a
25	MAZ	chr1:210406861-210407143	K562	blood:	n/a	n/a
26	SIN3AK20	chr1:210407010-210407229	SK-N-SH	brain:	n/a	n/a
27	EGR1	chr1:210406716-210407190	ECC-1	luminal epithelium:	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 chr1:210406907-210406917 chr1:210406903-210406917 chr1:210406905-210406919 chr1:210406895-210406905 chr1:210406907-210406916 chr1:210406906-210406916
28	POLR2A	chr1:210405595-210408558	H1-neurons	neurons:	n/a	n/a
29	FOS	chr1:210406974-210407585	HUVEC	blood vessel:	n/a	chr1:210407269-210407280
30	EP300	chr1:210407017-210407667	SK-N-SH_RA	brain:	n/a	chr1:210407457-210407467
31	RCOR1	chr1:210406879-210407084	K562	blood:	n/a	n/a
32	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
33	TEAD4	chr1:210406818-210407528	ECC-1	luminal epithelium:	n/a	n/a
34	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
35	NFIC	chr1:210406783-210407479	SK-N-SH	brain:	n/a	n/a
36	FOSL2	chr1:210406973-210407557	A549	lung:	n/a	n/a
37	TCF7L2	chr1:210406552-210407801	HCT-116	colon:	n/a	chr1:210407431-210407441
38	TBP	chr1:210406995-210407117	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr1:210406993-210407586	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr1:210406873-210407667	HUVEC	blood vessel:	n/a	n/a
41	SIN3AK20	chr1:210406690-210408118	MCF-7	breast:	n/a	n/a
42	CHD2	chr1:210406917-210407692	Hela-S3	cervix:	n/a	n/a
43	CTBP2	chr1:210405979-210407958	H1-hESC	embryonic stem cell:	n/a	n/a
44	E2F6	chr1:210406420-210407363	A549	lung:	n/a	chr1:210406562-210406577 chr1:210406950-210406960 chr1:210406620-210406632 chr1:210406572-210406581
45	POLR2A	chr1:210406832-210407767	HUVEC	blood vessel:	n/a	n/a
46	NFIC	chr1:210406783-210407872	SK-N-SH	brain:	n/a	n/a
47	TAF1	chr1:210406429-210407449	H1-neurons	neurons:	n/a	n/a
48	MAX	chr1:210406398-210407574	A549	lung:	n/a	chr1:210406540-210406549
49	MAX	chr1:210406319-210407751	A549	lung:	n/a	chr1:210406540-210406549
50	SMARCB1	chr1:210406546-210407922	Hela-S3	cervix:	n/a	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	chr1:210405867..210408909-chr1:210535692..210538632,3	MCF-7	breast:
4	chr1:210406407..210409749-chr1:210545963..210547821,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf133-2	chr1:210406980-210407466	NONHSAT009251
2	lnc-C1orf133-2	chr1:210406980-210407389	ENSG00000203706.4

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

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs624270	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs654523	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs656312	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs674513	0.88[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:119 , 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	chr1:210405200-210407600	Active TSS	NH-A	brain
4	chr1:210405400-210407600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:210405400-210407600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:210405400-210407600	Active TSS	Right Ventricle	heart
7	chr1:210405400-210407800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:210405400-210407800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:210405400-210407800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:210405400-210407800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr1:210405400-210407800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr1:210405400-210407800	Active TSS	Colon Smooth Muscle	Colon
13	chr1:210405400-210407800	Active TSS	Rectal Smooth Muscle	rectum
14	chr1:210405400-210408000	Bivalent Enhancer	Fetal Brain Male	brain
15	chr1:210405400-210408000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr1:210405600-210407400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:210405600-210407400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:210405600-210407400	Active TSS	HSMM	muscle
19	chr1:210405600-210407600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr1:210405600-210407600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:210405600-210407600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:210405600-210407600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:210405600-210407600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:210405600-210407600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
25	chr1:210405600-210407600	Active TSS	Brain Cingulate Gyrus	brain
26	chr1:210405600-210407600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr1:210405600-210407600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
28	chr1:210405600-210407600	Active TSS	Left Ventricle	heart
29	chr1:210405600-210407600	Active TSS	Ovary	ovary
30	chr1:210405600-210407600	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr1:210405600-210407600	Bivalent/Poised TSS	A549	lung
32	chr1:210405600-210407600	Active TSS	HSMMtube	muscle
33	chr1:210405600-210407600	Active TSS	NHLF	lung
34	chr1:210405600-210407800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:210405600-210407800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr1:210405600-210407800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:210405600-210407800	Active TSS	Aorta	Aorta
38	chr1:210405600-210407800	Active TSS	Brain Anterior Caudate	brain
39	chr1:210405600-210407800	Active TSS	Brain Substantia Nigra	brain
40	chr1:210405600-210407800	Active TSS	Placenta Amnion	Placenta Amnion
41	chr1:210405600-210407800	Active TSS	NHDF-Ad	bronchial
42	chr1:210405800-210407200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:210405800-210407400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:210405800-210407400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:210405800-210407400	Active TSS	Esophagus	oesophagus
46	chr1:210405800-210407400	Active TSS	NHEK	skin
47	chr1:210405800-210407600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:210405800-210407800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr1:210405800-210407800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:210405800-210407800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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