Variant report

Variant	rs58497973
Chromosome Location	chr1:197880935-197880936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr1:197877431-197889818	NT2-D1	testis:	n/a	n/a
2	MAX	chr1:197879954-197880974	H1-hESC	embryonic stem cell:	n/a	chr1:197880097-197880104 chr1:197880174-197880184 chr1:197880096-197880105 chr1:197880231-197880238 chr1:197880095-197880106 chr1:197880125-197880132
3	EGR1	chr1:197880470-197880989	H1-hESC	embryonic stem cell:	n/a	chr1:197880815-197880822
4	CTCF	chr1:197880840-197880990	SAEC	small airway:	n/a	chr1:197880842-197880855 chr1:197880841-197880851
5	YY1	chr1:197880476-197881119	H1-hESC	embryonic stem cell:	n/a	n/a
6	SUZ12	chr1:197877495-197890009	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr1:197880230-197880954	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTBP2	chr1:197879696-197883298	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:197880647-197882828	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr1:197880651-197883069	H1-neurons	neurons:	n/a	n/a
11	SP1	chr1:197880567-197880992	H1-hESC	embryonic stem cell:	n/a	chr1:197880754-197880765 chr1:197880735-197880746
12	SIN3A	chr1:197880597-197880970	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:197880923-197880973	NH-A	brain:	n/a
2	chr1:197880923-197880973	SK-N-SH_RA	brain:	n/a
3	chr1:197880923-197880973	LNCaP	prostate:	n/a
4	chr1:197880923-197880973	GM12892	blood:	n/a
5	chr1:197880923-197880973	HepG2	liver:	n/a
6	chr1:197880923-197880973	AG09319	gingival:	n/a
7	chr1:197880923-197880973	AG10803	skin:	n/a
8	chr1:197880923-197880973	SKMC	muscle:	n/a
9	chr1:197880923-197880973	HUVEC	blood vessel:	n/a
10	chr1:197880923-197880973	NB4	blood:	n/a
11	chr1:197880923-197880973	AG04449	skin:	fetal
12	chr1:197880923-197880973	MCF-7	breast:	n/a
13	chr1:197880923-197880973	CMK	blood:	n/a
14	chr1:197880923-197880973	BE2_C	brain:	n/a
15	chr1:197880923-197880973	AoSMC	blood vessel:	n/a
16	chr1:197880923-197880973	HRCEpiC	kidney:	n/a
17	chr1:197880923-197880973	HCT-116	colon:	n/a
18	chr1:197880923-197880973	HCPEpiC	choroid plexus:	n/a
19	chr1:197880923-197880973	NHDF-neo	bronchial:	n/a
20	chr1:197880923-197880973	PANC-1	pancreas:	n/a
21	chr1:197880923-197880973	PrEC	prostate:	n/a
22	chr1:197880923-197880973	Hela-S3	cervix:	n/a
23	chr1:197880923-197880973	HEEpiC	esophagus:	n/a
24	chr1:197880923-197880973	RPTEC	kidney:	n/a
25	chr1:197880923-197880973	GM19239	blood:	n/a
26	chr1:197880923-197880973	BJ	skin:	n/a
27	chr1:197880923-197880973	GM12891	blood:	n/a
28	chr1:197880923-197880973	Hepatocyte	liver:	n/a
29	chr1:197880923-197880973	Jurkat	blood:	n/a
30	chr1:197880923-197880973	H1-hESC	embryonic stem cell:	embryo
31	chr1:197880923-197880973	NT2-D1	testis:	n/a
32	chr1:197880923-197880973	HPAEpiC	pulmonary alveolar:	n/a
33	chr1:197880923-197880973	PFSK-1	brain:	n/a
34	chr1:197880923-197880973	HAEpiC	amniotic membrane:	n/a
35	chr1:197880923-197880973	ovcar-3	ovarian:	n/a
36	chr1:197880923-197880973	MCF10A-Er-Src	breast:	n/a
37	chr1:197880923-197880973	A549	lung:	n/a
38	chr1:197880923-197880973	HRE	kidney:	n/a
39	chr1:197880923-197880973	AG09309	skin:	n/a
40	chr1:197880923-197880973	AG04450	lung:	fetal
41	chr1:197880923-197880973	HL-60	blood:	n/a
42	chr1:197880923-197880973	HMEC	breast:	n/a
43	chr1:197880923-197880973	SAEC	small airway:	n/a
44	chr1:197880923-197880973	HEK293	kidney:	embryo
45	chr1:197880923-197880973	ProgFib	skin:	n/a
46	chr1:197880923-197880973	NHBE	bronchial:	n/a
47	chr1:197880923-197880973	U87	brain:	n/a
48	chr1:197880923-197880973	T-47D	breast:	n/a
49	chr1:197880923-197880973	HIPEpiC	eye:	n/a
50	chr1:197880923-197880973	Caco-2	colon:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197868383..197873929-chr1:197879774..197886951,11	K562	blood:

No data

Variant related genes	Relation type
LHX9	TF binding region
LHX9	CpG island
ENSG00000203724	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6692087	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73083807	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999662	chr1:197821769-197892803	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	esv2762214	chr1:197821769-197897496	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	14 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	chr1:197877400-197881600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:197877600-197883400	Bivalent Enhancer	Fetal Thymus	thymus
3	chr1:197877800-197881000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr1:197877800-197881400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
5	chr1:197877800-197882800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:197878800-197882800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:197879200-197881600	Bivalent Enhancer	Fetal Heart	heart
8	chr1:197879400-197881200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
9	chr1:197879400-197881600	Bivalent Enhancer	Fetal Lung	lung
10	chr1:197879400-197882800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr1:197879400-197882800	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr1:197879400-197882800	Enhancers	Pancreas	Pancrea
13	chr1:197879400-197883000	Bivalent Enhancer	Fetal Intestine Small	intestine
14	chr1:197879400-197883200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:197879600-197881000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
16	chr1:197879600-197881000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
17	chr1:197879600-197881200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:197879600-197881400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
19	chr1:197879600-197881400	Bivalent Enhancer	Brain Substantia Nigra	brain
20	chr1:197879600-197882000	Bivalent Enhancer	Placenta	Placenta
21	chr1:197879600-197882600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:197879600-197882800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
23	chr1:197879600-197882800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
24	chr1:197879600-197882800	Bivalent Enhancer	Spleen	Spleen
25	chr1:197879600-197883000	Bivalent Enhancer	Fetal Stomach	stomach
26	chr1:197879800-197881000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr1:197879800-197881000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
28	chr1:197879800-197881000	Bivalent/Poised TSS	Psoas Muscle	Psoas
29	chr1:197879800-197881200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
30	chr1:197879800-197881400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:197879800-197881400	Bivalent Enhancer	Esophagus	oesophagus
32	chr1:197879800-197882000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
33	chr1:197879800-197882400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr1:197879800-197882600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
35	chr1:197879800-197882800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
36	chr1:197879800-197882800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:197879800-197882800	Enhancers	Lung	lung
38	chr1:197879800-197882800	Bivalent Enhancer	Stomach Mucosa	stomach
39	chr1:197880000-197881000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:197880000-197881200	Flanking Active TSS	Right Ventricle	heart
41	chr1:197880000-197881600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
42	chr1:197880000-197881600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr1:197880000-197882800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:197880000-197882800	Enhancers	Gastric	stomach
45	chr1:197880000-197883000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
46	chr1:197880000-197883400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
47	chr1:197880000-197884800	Bivalent Enhancer	Fetal Brain Male	brain
48	chr1:197880200-197881000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
49	chr1:197880200-197881200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
50	chr1:197880200-197881200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell

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