Variant report

Variant	rs55904085
Chromosome Location	chr17:45000234-45000235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:411)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:411 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr17:44999732-45001057	H1-neurons	neurons:	n/a	n/a
2	ATF2	chr17:45000045-45000724	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr17:44999879-45001196	HepG2	liver:	n/a	n/a
4	MTA3	chr17:44999876-45000713	GM12878	blood:	n/a	n/a
5	TBP	chr17:45000007-45001084	HepG2	liver:	n/a	n/a
6	CHD2	chr17:45000071-45000765	HepG2	liver:	n/a	n/a
7	TAF1	chr17:45000008-45000794	GM12892	blood:	n/a	n/a
8	MTA3	chr17:44999894-45000913	GM12878	blood:	n/a	n/a
9	MAX	chr17:44999912-45000807	ECC-1	luminal epithelium:	n/a	chr17:45000630-45000641 chr17:45000791-45000800
10	HEY1	chr17:44999996-45000951	K562	blood:	n/a	n/a
11	POLR2A	chr17:45000085-45000730	A549	lung:	n/a	n/a
12	CEBPB	chr17:45000187-45000626	HepG2	liver:	n/a	n/a
13	POLR2A	chr17:44999909-45001055	K562	blood:	n/a	n/a
14	POLR2A	chr17:44999993-45001134	GM12878	blood:	n/a	n/a
15	POLR2A	chr17:44999932-45000977	HCT-116	colon:	n/a	n/a
16	ELK1	chr17:45000163-45000736	GM12878	blood:	n/a	n/a
17	BHLHE40	chr17:44999990-45000920	K562	blood:	n/a	n/a
18	POLR2A	chr17:44999956-45000919	GM19099	blood:	n/a	n/a
19	CBX3	chr17:44999765-45000731	K562	blood:	n/a	n/a
20	SIX5	chr17:44999827-45000968	A549	lung:	n/a	chr17:44999885-44999894 chr17:44999883-44999897
21	POLR2A	chr17:45000016-45000935	GM12878	blood:	n/a	n/a
22	TCF7L2	chr17:45000037-45000539	Hela-S3	cervix:	n/a	n/a
23	PAX5	chr17:45000154-45000679	GM12878	blood:	n/a	n/a
24	ELF1	chr17:45000003-45000806	MCF-7	breast:	n/a	chr17:45000086-45000097 chr17:45000485-45000496
25	POLR2A	chr17:44999972-45001123	GM12878	blood:	n/a	n/a
26	BCLAF1	chr17:44999865-45000789	GM12878	blood:	n/a	chr17:45000541-45000554
27	TAF1	chr17:45000017-45000849	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYBL2	chr17:44999856-45000922	HepG2	liver:	n/a	n/a
29	MAX	chr17:44999927-45000885	MCF-7	breast:	n/a	chr17:45000630-45000641 chr17:45000791-45000800
30	IRF4	chr17:45000044-45000591	GM12878	blood:	n/a	n/a
31	POLR2A	chr17:45000008-45000890	Hela-S3	cervix:	n/a	n/a
32	NR3C1	chr17:45000111-45000681	A549	lung:	n/a	n/a
33	ZNF143	chr17:45000031-45000738	GM12878	blood:	n/a	n/a
34	POLR2A	chr17:45000005-45001086	GM12891	blood:	n/a	n/a
35	RFX5	chr17:45000205-45000519	K562	blood:	n/a	n/a
36	POLR2A	chr17:44999905-45001314	MCF10A-Er-Src	breast:	n/a	n/a
37	YY1	chr17:45000065-45000802	A549	lung:	n/a	chr17:45000541-45000555
38	GABPA	chr17:45000099-45000874	HepG2	liver:	n/a	chr17:45000606-45000615
39	GABPA	chr17:45000234-45000798	GM12878	blood:	n/a	chr17:45000606-45000615
40	REST	chr17:45000024-45000947	A549	lung:	n/a	n/a
41	POLR2A	chr17:45000027-45000965	GM12891	blood:	n/a	n/a
42	NFIC	chr17:44999983-45000769	HepG2	liver:	n/a	n/a
43	REST	chr17:45000059-45000838	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr17:44999967-45000782	K562	blood:	n/a	n/a
45	TAF1	chr17:44999994-45000841	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr17:44999955-45000727	GM12892	blood:	n/a	n/a
47	TAF1	chr17:44999941-45000925	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr17:45000055-45000751	HepG2	liver:	n/a	n/a
49	TAF1	chr17:45000056-45000799	K562	blood:	n/a	n/a
50	YY1	chr17:45000081-45000784	GM12878	blood:	n/a	chr17:45000541-45000555

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:45000220-45000270	IMR90	lung:	fetal
2	chr17:45000220-45000270	GM12891	blood:	n/a
3	chr17:45000220-45000270	PFSK-1	brain:	n/a
4	chr17:45000220-45000270	SAEC	small airway:	n/a
5	chr17:45000220-45000270	SK-N-SH_RA	brain:	n/a
6	chr17:45000220-45000270	HEEpiC	esophagus:	n/a
7	chr17:45000220-45000270	GM19239	blood:	n/a
8	chr17:45000220-45000270	HCT-116	colon:	n/a
9	chr17:45000220-45000270	HPAEpiC	pulmonary alveolar:	n/a
10	chr17:45000220-45000270	CMK	blood:	n/a
11	chr17:45000220-45000270	ProgFib	skin:	n/a
12	chr17:45000220-45000270	PrEC	prostate:	n/a
13	chr17:45000220-45000270	SK-N-SH	brain:	n/a
14	chr17:45000220-45000270	NB4	blood:	n/a
15	chr17:45000220-45000270	PANC-1	pancreas:	n/a
16	chr17:45000220-45000270	HRCEpiC	kidney:	n/a
17	chr17:45000220-45000270	AG04449	skin:	fetal
18	chr17:45000220-45000270	HMEC	breast:	n/a
19	chr17:45000220-45000270	HCF	heart:	n/a
20	chr17:45000220-45000270	Caco-2	colon:	n/a
21	chr17:45000220-45000270	Jurkat	blood:	n/a
22	chr17:45000220-45000270	MCF10A-Er-Src	breast:	n/a
23	chr17:45000220-45000270	AG04450	lung:	fetal
24	chr17:45000220-45000270	HUVEC	blood vessel:	n/a
25	chr17:45000220-45000270	GM12892	blood:	n/a
26	chr17:45000220-45000270	HAEpiC	amniotic membrane:	n/a
27	chr17:45000220-45000270	HCM	heart:	n/a
28	chr17:45000220-45000270	SK-N-MC	brain:	n/a
29	chr17:45000220-45000270	HL-60	blood:	n/a
30	chr17:45000220-45000270	A549	lung:	n/a
31	chr17:45000220-45000270	HepG2	liver:	n/a
32	chr17:45000220-45000270	NH-A	brain:	n/a
33	chr17:45000220-45000270	AG09309	skin:	n/a
34	chr17:45000220-45000270	HRE	kidney:	n/a
35	chr17:45000220-45000270	HIPEpiC	eye:	n/a
36	chr17:45000220-45000270	RPTEC	kidney:	n/a
37	chr17:45000220-45000270	HCPEpiC	choroid plexus:	n/a
38	chr17:45000220-45000270	ovcar-3	ovarian:	n/a
39	chr17:45000220-45000270	BE2_C	brain:	n/a
40	chr17:45000220-45000270	HNPCEpiC	eye:	n/a
41	chr17:45000220-45000270	AG10803	skin:	n/a
42	chr17:45000220-45000270	HEK293	kidney:	embryo
43	chr17:45000220-45000270	T-47D	breast:	n/a
44	chr17:45000220-45000270	HRPEpiC	eye:	n/a
45	chr17:45000220-45000270	NHBE	bronchial:	n/a
46	chr17:45000220-45000270	SKMC	muscle:	n/a
47	chr17:45000220-45000270	NT2-D1	testis:	n/a
48	chr17:45000220-45000270	Hepatocyte	liver:	n/a
49	chr17:45000220-45000270	BJ	skin:	n/a
50	chr17:45000220-45000270	H1-hESC	embryonic stem cell:	embryo

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:44999992..45001971-chr17:45015932..45018557,3	MCF-7	breast:
2	chr17:44995313..44999079-chr17:44999263..45002356,3	MCF-7	breast:
3	chr15:44089561..44091456-chr17:44999592..45001929,2	MCF-7	breast:
4	chr17:45000165..45000665-chr6:20401996..20402497,2	NB4	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPRML-1	chr17:45000177-45000400	ENSG00000261886.1

No data

Variant related genes	Relation type
GOSR2	TF binding region
ENSG00000262633	TF binding region
ENSG00000262633	CpG island
GOSR2	CpG island
ENSG00000108433	Chromatin interaction
ENSG00000184716	Chromatin interaction
ENSG00000210709	Chromatin interaction
ENSG00000112242	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12452813	1.00[EUR][1000 genomes]
rs12452830	1.00[EUR][1000 genomes]
rs12453371	1.00[EUR][1000 genomes]
rs12453477	1.00[EUR][1000 genomes]
rs12453953	1.00[EUR][1000 genomes]
rs16941159	1.00[EUR][1000 genomes]
rs34577788	1.00[EUR][1000 genomes]
rs55807756	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60653820	0.85[AFR][1000 genomes]
rs7210725	1.00[EUR][1000 genomes]
rs7215497	1.00[EUR][1000 genomes]
rs7218079	1.00[EUR][1000 genomes]
rs7224871	1.00[EUR][1000 genomes]
rs73988218	0.85[AFR][1000 genomes]
rs8075445	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv428672	chr17:44872446-45023425	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:44999400-45001200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr17:44999400-45001400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:44999600-45000400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr17:44999600-45000600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr17:44999600-45000600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr17:44999600-45000800	Active TSS	Fetal Brain Female	brain
7	chr17:44999600-45001200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr17:44999600-45001200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr17:44999600-45001200	Active TSS	Brain Anterior Caudate	brain
10	chr17:44999600-45001200	Active TSS	Brain Cingulate Gyrus	brain
11	chr17:44999600-45001200	Active TSS	Duodenum Mucosa	Duodenum
12	chr17:44999600-45001200	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr17:44999600-45001400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr17:44999600-45001400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:44999600-45001400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr17:44999600-45001400	Active TSS	Stomach Smooth Muscle	stomach
17	chr17:44999600-45001800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr17:44999600-45002000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr17:44999600-45002200	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr17:44999800-45000400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr17:44999800-45000800	Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr17:44999800-45000800	Active TSS	Primary B cells from cord blood	blood
23	chr17:44999800-45000800	Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr17:44999800-45000800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr17:44999800-45000800	Active TSS	Monocytes-CD14+_RO01746	blood
26	chr17:44999800-45001000	Active TSS	Primary monocytes fromperipheralblood	blood
27	chr17:44999800-45001000	Active TSS	Primary B cells from peripheral blood	blood
28	chr17:44999800-45001000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr17:44999800-45001000	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr17:44999800-45001000	Active TSS	Adipose Nuclei	Adipose
31	chr17:44999800-45001000	Active TSS	Liver	Liver
32	chr17:44999800-45001000	Active TSS	Brain Substantia Nigra	brain
33	chr17:44999800-45001000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr17:44999800-45001000	Active TSS	Fetal Lung	lung
35	chr17:44999800-45001000	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr17:44999800-45001200	Active TSS	Primary T cells fromperipheralblood	blood
37	chr17:44999800-45001200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr17:44999800-45001200	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr17:44999800-45001200	Active TSS	Brain Germinal Matrix	brain
40	chr17:44999800-45001200	Active TSS	Brain Hippocampus Middle	brain
41	chr17:44999800-45001200	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr17:44999800-45001200	Active TSS	Fetal Muscle Leg	muscle
43	chr17:44999800-45001200	Active TSS	Placenta	Placenta
44	chr17:44999800-45001200	Active TSS	Fetal Stomach	stomach
45	chr17:44999800-45001200	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr17:44999800-45001200	Active TSS	Dnd41	blood
47	chr17:44999800-45001200	Active TSS	HUVEC	blood vessel
48	chr17:44999800-45001200	Active TSS	NH-A	brain
49	chr17:44999800-45001200	Active TSS	NHEK	skin
50	chr17:44999800-45001400	Active TSS	ES-I3 Cell Line	embryonic stem cell

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