Variant report

Variant	rs56397999
Chromosome Location	chr1:210502088-210502089
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	POU2F2	chr1:210501841-210502515	GM12878	blood:	n/a	chr1:210502166-210502178
2	POLR2A	chr1:210501952-210502472	H1-neurons	neurons:	n/a	n/a
3	CTCF	chr1:210502060-210502210	HepG2	liver:	n/a	chr1:210502165-210502178
4	CTCF	chr1:210502060-210502210	AG04449	skin:	n/a	chr1:210502165-210502178
5	CTCF	chr1:210502080-210502230	GM12873	blood:	n/a	chr1:210502165-210502178
6	TAF1	chr1:210501934-210502855	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:210501985-210503130	GM12878	blood:	n/a	n/a
8	CTCF	chr1:210502040-210502190	HRPEpiC	eye:	n/a	chr1:210502165-210502178
9	POLR2A	chr1:210501914-210502856	ProgFib	skin:	n/a	n/a
10	POLR2A	chr1:210501883-210503031	GM12878	blood:	n/a	n/a
11	RFX5	chr1:210502011-210502579	GM12878	blood:	n/a	n/a
12	RAD21	chr1:210502037-210502379	H1-hESC	embryonic stem cell:	n/a	chr1:210502164-210502177 chr1:210502338-210502352 chr1:210502165-210502175
13	CTCF	chr1:210502060-210502210	Hela-S3	cervix:	n/a	chr1:210502165-210502178
14	POLR2A	chr1:210501989-210502676	PANC-1	pancreas:	n/a	n/a
15	CTCF	chr1:210501940-210502170	HRE	kidney:	n/a	n/a
16	POLR2A	chr1:210502010-210502838	A549	lung:	n/a	n/a
17	POLR2A	chr1:210501985-210502857	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:210501956-210502958	HCT-116	colon:	n/a	n/a
19	CTCF	chr1:210502060-210502210	GM12878	blood:	n/a	chr1:210502165-210502178
20	CTCF	chr1:210501980-210502130	HA-sp	spinal cord:	n/a	n/a
21	POLR2A	chr1:210501928-210502906	A549	lung:	n/a	n/a
22	POLR2A	chr1:210501859-210503137	GM12891	blood:	n/a	n/a
23	MAX	chr1:210501714-210503137	A549	lung:	n/a	n/a
24	TAF1	chr1:210502003-210502413	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:210501934-210503014	MCF-7	breast:	n/a	n/a
26	E2F4	chr1:210501813-210503029	MCF10A-Er-Src	breast:	n/a	chr1:210502342-210502352 chr1:210502579-210502591 chr1:210502163-210502172
27	POLR2A	chr1:210501914-210503003	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:210501966-210503031	HUVEC	blood vessel:	n/a	n/a
29	YY1	chr1:210501989-210502526	GM12878	blood:	n/a	chr1:210502424-210502433 chr1:210502253-210502264 chr1:210502235-210502249 chr1:210502339-210502353 chr1:210502338-210502349 chr1:210502419-210502433
30	POLR2A	chr1:210501905-210503020	SK-N-SH	brain:	n/a	n/a
31	MAX	chr1:210501848-210503014	A549	lung:	n/a	n/a
32	PAX5	chr1:210501996-210502457	GM12892	blood:	n/a	chr1:210502240-210502249
33	POLR2A	chr1:210501989-210502208	U87	brain:	n/a	n/a
34	RELA	chr1:210501928-210503105	GM18951	blood:	n/a	n/a
35	POLR2A	chr1:210501858-210502860	A549	lung:	n/a	n/a
36	POLR2A	chr1:210501769-210503128	GM12878	blood:	n/a	n/a
37	TCF12	chr1:210501839-210503028	A549	lung:	n/a	n/a
38	CREB1	chr1:210501940-210502691	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:210501979-210502985	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr1:210501846-210503033	GM12892	blood:	n/a	n/a
41	POLR2A	chr1:210502021-210502915	HUVEC	blood vessel:	n/a	n/a
42	YY1	chr1:210502048-210502350	HCT-116	colon:	n/a	chr1:210502253-210502264 chr1:210502235-210502249 chr1:210502338-210502349
43	TCF7L2	chr1:210501933-210502877	HCT-116	colon:	n/a	n/a
44	CTCF	chr1:210502020-210502170	SAEC	small airway:	n/a	n/a
45	CTCF	chr1:210502080-210502230	HUVEC	blood vessel:	n/a	chr1:210502165-210502178
46	POLR2A	chr1:210501939-210502985	HCT-116	colon:	n/a	n/a
47	TAF1	chr1:210502024-210503000	A549	lung:	n/a	n/a
48	CTCF	chr1:210502060-210502210	AG09309	skin:	n/a	chr1:210502165-210502178
49	CHD1	chr1:210501841-210502785	GM12878	blood:	n/a	n/a
50	CTCF	chr1:210502060-210502210	GM12873	blood:	n/a	chr1:210502165-210502178

No.	Distal block	Cell Line	Cell type
1	chr1:210499300..210503346-chr1:210545682..210548805,5	K562	blood:
2	chr1:210497683..210507034-chr1:210544536..210549319,22	MCF-7	breast:
3	chr1:210501785..210502375-chr10:12170815..12171747,2	HCT-116	colon:
4	chr1:210498648..210506320-chr1:210545155..210548300,7	K562	blood:
5	chr1:210498783..210502429-chr1:210544443..210548917,7	MCF-7	breast:

Variant related genes	Relation type
HHAT	TF binding region
ENSG00000200972	Chromatin interaction
ENSG00000065665	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11119446	1.00[EUR][1000 genomes]
rs55792645	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55884682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56215802	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59742593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs621684	1.00[EUR][1000 genomes]
rs653935	1.00[EUR][1000 genomes]
rs663132	1.00[EUR][1000 genomes]
rs663987	1.00[EUR][1000 genomes]
rs685743	1.00[EUR][1000 genomes]
rs73074137	1.00[EUR][1000 genomes]
rs74156132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74156134	1.00[AMR][1000 genomes]
rs74156135	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210501400-210502200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr1:210501400-210502200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:210501400-210502200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:210501400-210502200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:210501400-210502200	Flanking Active TSS	Dnd41	blood
6	chr1:210501400-210502200	Flanking Active TSS	HMEC	breast
7	chr1:210501400-210502400	Enhancers	Fetal Brain Male	brain
8	chr1:210501400-210502800	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr1:210501600-210502200	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr1:210501600-210502200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr1:210501600-210502200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:210501600-210502200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr1:210501600-210502200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:210501600-210502200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:210501600-210502200	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr1:210501600-210502200	Flanking Active TSS	Liver	Liver
17	chr1:210501600-210502200	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr1:210501600-210502800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:210501600-210502800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr1:210501600-210502800	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr1:210501600-210502800	Active TSS	HSMMtube	muscle
22	chr1:210501600-210503000	Active TSS	A549	lung
23	chr1:210501600-210503200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:210501600-210503200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:210501600-210503200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:210501600-210503200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr1:210501600-210503200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:210501600-210503200	Active TSS	Fetal Brain Female	brain
29	chr1:210501600-210503400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr1:210501800-210502200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:210501800-210502200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:210501800-210502200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:210501800-210502200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr1:210501800-210502200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr1:210501800-210502200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:210501800-210502200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:210501800-210502200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:210501800-210502200	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr1:210501800-210502200	Flanking Active TSS	Esophagus	oesophagus
40	chr1:210501800-210502200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr1:210501800-210502200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr1:210501800-210502200	Flanking Active TSS	HUVEC	blood vessel
43	chr1:210501800-210502200	Flanking Active TSS	NHLF	lung
44	chr1:210501800-210502600	Active TSS	Spleen	Spleen
45	chr1:210501800-210502800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr1:210501800-210502800	Active TSS	NH-A	brain
47	chr1:210501800-210502800	Active TSS	Osteobl	bone
48	chr1:210501800-210503000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:210501800-210503000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr1:210501800-210503000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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