Variant report

Variant	rs539342126
Chromosome Location	chr1:210406202-210406203
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	POLR2A	chr1:210405928-210406412	HUVEC	blood vessel:	n/a	n/a
2	FOXP2	chr1:210405949-210406210	SK-N-MC	brain:	n/a	n/a
3	MAX	chr1:210405826-210406208	MCF-7	breast:	n/a	n/a
4	MAX	chr1:210405600-210406261	A549	lung:	n/a	n/a
5	POLR2A	chr1:210405974-210406390	MCF-7	breast:	n/a	n/a
6	TCF12	chr1:210405238-210406224	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:210406044-210406353	ProgFib	skin:	n/a	n/a
8	FOXA1	chr1:210405940-210406248	T-47D	breast:	n/a	n/a
9	FOXM1	chr1:210405982-210406280	MCF-7	breast:	n/a	n/a
10	SIN3A	chr1:210405997-210406256	H1-hESC	embryonic stem cell:	n/a	n/a
11	MXI1	chr1:210406047-210406213	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAZ	chr1:210405793-210408090	IMR90	lung:	n/a	chr1:210406540-210406549
13	NFIC	chr1:210406031-210406419	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr1:210405815-210406417	H1-neurons	neurons:	n/a	n/a
15	TAF1	chr1:210405955-210406338	H1-neurons	neurons:	n/a	n/a
16	HDAC2	chr1:210405830-210406259	MCF-7	breast:	n/a	n/a
17	MAX	chr1:210405418-210406263	SK-N-SH	brain:	n/a	n/a
18	GATA3	chr1:210405749-210406245	MCF-7	breast:	n/a	chr1:210405778-210405786
19	POLR2A	chr1:210405595-210408558	H1-neurons	neurons:	n/a	n/a
20	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
21	ZNF263	chr1:210405983-210406298	HEK293-T-REx	kidney:	n/a	n/a
22	PBX3	chr1:210405387-210406376	SK-N-SH	brain:	n/a	n/a
23	CTBP2	chr1:210405979-210407958	H1-hESC	embryonic stem cell:	n/a	n/a
24	GATA3	chr1:210405916-210406280	T-47D	breast:	n/a	n/a
25	NR2F2	chr1:210405815-210406244	MCF-7	breast:	n/a	n/a
26	REST	chr1:210405752-210406358	H1-neurons	neurons:	n/a	n/a
27	EP300	chr1:210405319-210406323	SK-N-SH	brain:	n/a	chr1:210405510-210405524 chr1:210405976-210405985 chr1:210405975-210405991 chr1:210405979-210405988 chr1:210405511-210405525 chr1:210405561-210405570
28	POLR2A	chr1:210406098-210406307	H1-hESC	embryonic stem cell:	n/a	n/a
29	REST	chr1:210405235-210408055	H1-neurons	neurons:	n/a	n/a
30	MYC	chr1:210405998-210406203	MCF-7	breast:	n/a	n/a
31	EP300	chr1:210405923-210406287	T-47D	breast:	n/a	chr1:210405976-210405985 chr1:210405975-210405991 chr1:210405979-210405988
32	SIN3AK20	chr1:210405672-210406382	MCF-7	breast:	n/a	n/a
33	EP300	chr1:210405899-210406319	T-47D	breast:	n/a	chr1:210405976-210405985 chr1:210405975-210405991 chr1:210405979-210405988
34	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
35	CTCF	chr1:210406120-210406270	NHEK	skin:	n/a	n/a
36	POLR2A	chr1:210405931-210407316	MCF-7	breast:	n/a	n/a
37	POLR2A	chr1:210405721-210407760	HUVEC	blood vessel:	n/a	n/a
38	BACH1	chr1:210405970-210407150	H1-hESC	embryonic stem cell:	n/a	n/a
39	GATA3	chr1:210405943-210406286	T-47D	breast:	n/a	n/a
40	MAX	chr1:210405915-210406350	ECC-1	luminal epithelium:	n/a	n/a
41	SIN3AK20	chr1:210405904-210406217	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr1:210406073-210406840	HUVEC	blood vessel:	n/a	n/a
43	CCNT2	chr1:210406103-210406312	K562	blood:	n/a	n/a
44	TCF12	chr1:210405200-210408026	SK-N-SH	brain:	n/a	chr1:210407710-210407720
45	MAX	chr1:210405928-210406574	ECC-1	luminal epithelium:	n/a	chr1:210406540-210406549
46	POLR2A	chr1:210405984-210406411	MCF-7	breast:	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	chr1:210404553..210406882-chr6:30538400..30541136,2	MCF-7	breast:
4	chr1:210405867..210408909-chr1:210535692..210538632,3	MCF-7	breast:

Variant related genes	Relation type
SERTAD4	TF binding region
ENSG00000054392	Chromatin interaction
ENSG00000204574	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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:109 , 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	chr1:210405200-210406400	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr1:210405200-210406600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:210405200-210407600	Active TSS	NH-A	brain
6	chr1:210405400-210406400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:210405400-210406400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:210405400-210406400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
9	chr1:210405400-210406600	Active TSS	Muscle Satellite Cultured Cells	--
10	chr1:210405400-210407600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:210405400-210407600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr1:210405400-210407600	Active TSS	Right Ventricle	heart
13	chr1:210405400-210407800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:210405400-210407800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:210405400-210407800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr1:210405400-210407800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr1:210405400-210407800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr1:210405400-210407800	Active TSS	Colon Smooth Muscle	Colon
19	chr1:210405400-210407800	Active TSS	Rectal Smooth Muscle	rectum
20	chr1:210405400-210408000	Bivalent Enhancer	Fetal Brain Male	brain
21	chr1:210405400-210408000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:210405600-210406400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
23	chr1:210405600-210406600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:210405600-210406600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:210405600-210406600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:210405600-210406600	Bivalent Enhancer	Primary T cells from cord blood	blood
27	chr1:210405600-210406600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
28	chr1:210405600-210406600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
29	chr1:210405600-210406600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:210405600-210406600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
31	chr1:210405600-210406600	Active TSS	HMEC	breast
32	chr1:210405600-210406600	Bivalent/Poised TSS	Osteobl	bone
33	chr1:210405600-210406800	Flanking Bivalent TSS/Enh	Thymus	Thymus
34	chr1:210405600-210407000	Active TSS	Colonic Mucosa	Colon
35	chr1:210405600-210407000	Bivalent Enhancer	Fetal Lung	lung
36	chr1:210405600-210407000	Active TSS	Right Atrium	heart
37	chr1:210405600-210407400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:210405600-210407400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:210405600-210407400	Active TSS	HSMM	muscle
40	chr1:210405600-210407600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr1:210405600-210407600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:210405600-210407600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:210405600-210407600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:210405600-210407600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:210405600-210407600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
46	chr1:210405600-210407600	Active TSS	Brain Cingulate Gyrus	brain
47	chr1:210405600-210407600	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr1:210405600-210407600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
49	chr1:210405600-210407600	Active TSS	Left Ventricle	heart
50	chr1:210405600-210407600	Active TSS	Ovary	ovary

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