Variant report

Variant	rs2473814
Chromosome Location	chr1:210405907-210405908
allele	C/G
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	MAX	chr1:210405826-210406208	MCF-7	breast:	n/a	n/a
2	MAX	chr1:210405600-210406261	A549	lung:	n/a	n/a
3	TCF12	chr1:210405238-210406224	SK-N-SH	brain:	n/a	n/a
4	MAZ	chr1:210405793-210408090	IMR90	lung:	n/a	chr1:210406540-210406549
5	POLR2A	chr1:210405815-210406417	H1-neurons	neurons:	n/a	n/a
6	HDAC2	chr1:210405830-210406259	MCF-7	breast:	n/a	n/a
7	MAX	chr1:210405418-210406263	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr1:210405749-210406245	MCF-7	breast:	n/a	chr1:210405778-210405786
9	POLR2A	chr1:210405595-210408558	H1-neurons	neurons:	n/a	n/a
10	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
11	PBX3	chr1:210405387-210406376	SK-N-SH	brain:	n/a	n/a
12	NR2F2	chr1:210405815-210406244	MCF-7	breast:	n/a	n/a
13	REST	chr1:210405752-210406358	H1-neurons	neurons:	n/a	n/a
14	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
15	REST	chr1:210405235-210408055	H1-neurons	neurons:	n/a	n/a
16	SIN3AK20	chr1:210405672-210406382	MCF-7	breast:	n/a	n/a
17	EP300	chr1:210405899-210406319	T-47D	breast:	n/a	chr1:210405976-210405985 chr1:210405975-210405991 chr1:210405979-210405988
18	POLR2A	chr1:210405721-210407760	HUVEC	blood vessel:	n/a	n/a
19	SIN3AK20	chr1:210405904-210406217	SK-N-SH	brain:	n/a	n/a
20	TCF12	chr1:210405200-210408026	SK-N-SH	brain:	n/a	chr1:210407710-210407720

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: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10863816	0.86[EUR][1000 genomes]
rs11119444	0.83[EUR][1000 genomes]
rs12239420	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1338298	0.86[EUR][1000 genomes]
rs1473696	0.86[EUR][1000 genomes]
rs2473813	0.90[EUR][1000 genomes]
rs2494185	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2494186	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4844981	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs624270	0.93[ASN][1000 genomes]
rs654523	0.89[ASN][1000 genomes]
rs656312	0.88[ASN][1000 genomes]
rs660611	0.87[ASN][1000 genomes]
rs674513	0.88[ASN][1000 genomes]
rs677520	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7534368	0.85[EUR][1000 genomes]
rs845451	0.84[ASN][1000 genomes]
rs910109	0.88[EUR][1000 genomes]
rs910110	0.88[EUR][1000 genomes]
rs9429839	0.88[EUR][1000 genomes]
rs9430037	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][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:97 , 50 per page) page: 1 2

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	chr1:210405400-210406000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:210405400-210406000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
8	chr1:210405400-210406400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:210405400-210406400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:210405400-210406400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
11	chr1:210405400-210406600	Active TSS	Muscle Satellite Cultured Cells	--
12	chr1:210405400-210407600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:210405400-210407600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:210405400-210407600	Active TSS	Right Ventricle	heart
15	chr1:210405400-210407800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:210405400-210407800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:210405400-210407800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr1:210405400-210407800	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr1:210405400-210407800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr1:210405400-210407800	Active TSS	Colon Smooth Muscle	Colon
21	chr1:210405400-210407800	Active TSS	Rectal Smooth Muscle	rectum
22	chr1:210405400-210408000	Bivalent Enhancer	Fetal Brain Male	brain
23	chr1:210405400-210408000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr1:210405600-210406000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:210405600-210406000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
26	chr1:210405600-210406000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
27	chr1:210405600-210406000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:210405600-210406000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:210405600-210406000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
30	chr1:210405600-210406200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:210405600-210406200	Active TSS	Psoas Muscle	Psoas
32	chr1:210405600-210406400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
33	chr1:210405600-210406600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:210405600-210406600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:210405600-210406600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:210405600-210406600	Bivalent Enhancer	Primary T cells from cord blood	blood
37	chr1:210405600-210406600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr1:210405600-210406600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
39	chr1:210405600-210406600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:210405600-210406600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
41	chr1:210405600-210406600	Active TSS	HMEC	breast
42	chr1:210405600-210406600	Bivalent/Poised TSS	Osteobl	bone
43	chr1:210405600-210406800	Flanking Bivalent TSS/Enh	Thymus	Thymus
44	chr1:210405600-210407000	Active TSS	Colonic Mucosa	Colon
45	chr1:210405600-210407000	Bivalent Enhancer	Fetal Lung	lung
46	chr1:210405600-210407000	Active TSS	Right Atrium	heart
47	chr1:210405600-210407400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:210405600-210407400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:210405600-210407400	Active TSS	HSMM	muscle
50	chr1:210405600-210407600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell

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