Variant report

Variant	rs28623237
Chromosome Location	chr17:38080947-38080948
allele	C/T
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	CTCF	chr17:38080800-38080950	HBMEC	blood vessel:	n/a	chr17:38080867-38080876
2	WRNIP1	chr17:38080496-38081128	GM12878	blood:	n/a	n/a
3	CTCF	chr17:38080778-38081035	H1-hESC	embryonic stem cell:	n/a	chr17:38080867-38080876
4	CTCF	chr17:38080824-38080951	K562	blood:	n/a	chr17:38080867-38080876
5	HEY1	chr17:38080216-38082094	HepG2	liver:	n/a	n/a
6	POLR2A	chr17:38080274-38081435	HepG2	liver:	n/a	n/a
7	ARID3A	chr17:38080421-38081000	HepG2	liver:	n/a	n/a
8	EP300	chr17:38080369-38080956	HepG2	liver:	n/a	chr17:38080651-38080660
9	CTCF	chr17:38080800-38080950	HRE	kidney:	n/a	chr17:38080867-38080876
10	CTCF	chr17:38080820-38080970	HPF	lung:	n/a	chr17:38080867-38080876
11	CTCF	chr17:38080900-38081050	WI-38	lung:	n/a	n/a
12	EP300	chr17:38080260-38081010	HepG2	liver:	n/a	chr17:38080651-38080660
13	CTCF	chr17:38080776-38080973	HUVEC	blood vessel:	n/a	chr17:38080867-38080876
14	CTCF	chr17:38080820-38080970	HVMF	connective:	n/a	chr17:38080867-38080876
15	RAD21	chr17:38080434-38080962	HepG2	liver:	n/a	n/a
16	CTCF	chr17:38080809-38080953	GM19238	blood:	n/a	chr17:38080867-38080876
17	SPI1	chr17:38080927-38081201	GM12878	blood:	n/a	chr17:38080935-38080948
18	TEAD4	chr17:38080232-38081076	HepG2	liver:	n/a	n/a
19	CTCF	chr17:38080840-38080990	NHDF-neo	bronchial:	n/a	chr17:38080867-38080876
20	RXRA	chr17:38080293-38080969	HepG2	liver:	n/a	n/a
21	POLR2A	chr17:38080178-38081096	HepG2	liver:	n/a	n/a
22	RXRA	chr17:38080220-38081044	HepG2	liver:	n/a	chr17:38080982-38080998
23	CTCF	chr17:38080722-38080972	HepG2	liver:	n/a	chr17:38080867-38080876
24	CTCF	chr17:38080800-38080950	HepG2	liver:	n/a	chr17:38080867-38080876
25	HDAC2	chr17:38080378-38080969	HepG2	liver:	n/a	n/a
26	CTCF	chr17:38080840-38080990	NHLF	lung:	n/a	chr17:38080867-38080876
27	MAX	chr17:38079938-38081235	HepG2	liver:	n/a	chr17:38080785-38080795
28	CTCF	chr17:38080800-38080950	HA-sp	spinal cord:	n/a	chr17:38080867-38080876
29	MYBL2	chr17:38079953-38081220	HepG2	liver:	n/a	n/a
30	MBD4	chr17:38080266-38081060	HepG2	liver:	n/a	n/a
31	CTCF	chr17:38080800-38080950	GM12873	blood:	n/a	chr17:38080867-38080876
32	NFIC	chr17:38080184-38081073	HepG2	liver:	n/a	n/a
33	CTCF	chr17:38080800-38080950	Caco-2	colon:	n/a	chr17:38080867-38080876
34	HNF4G	chr17:38080239-38080967	HepG2	liver:	n/a	n/a
35	CTCF	chr17:38080800-38080950	AG10803	skin:	n/a	chr17:38080867-38080876
36	MBD4	chr17:38080268-38081125	HepG2	liver:	n/a	n/a
37	SPI1	chr17:38080876-38081200	GM12891	blood:	n/a	chr17:38080935-38080948
38	CTCF	chr17:38080840-38080990	HRPEpiC	eye:	n/a	chr17:38080867-38080876
39	MXI1	chr17:38079912-38080952	IMR90	lung:	n/a	n/a
40	CTCF	chr17:38080840-38080990	HA-sp	spinal cord:	n/a	chr17:38080867-38080876
41	CTCF	chr17:38080739-38080985	IMR90	lung:	n/a	chr17:38080867-38080876
42	POLR2A	chr17:38080171-38081057	GM12878	blood:	n/a	n/a
43	HNF4G	chr17:38080298-38081226	HepG2	liver:	n/a	chr17:38081129-38081143
44	CTCF	chr17:38080860-38081010	RPTEC	kidney:	n/a	chr17:38080867-38080876
45	CTCF	chr17:38080820-38080970	HBMEC	blood vessel:	n/a	chr17:38080867-38080876
46	CTCF	chr17:38080800-38080950	AoAF	blood vessel:	n/a	chr17:38080867-38080876
47	CTCF	chr17:38080738-38081037	GM12878	blood:	n/a	chr17:38080867-38080876
48	SMC3	chr17:38080542-38081079	HepG2	liver:	n/a	n/a
49	CTCF	chr17:38080800-38080950	AG09319	gingival:	n/a	chr17:38080867-38080876
50	CTCF	chr17:38080817-38080968	GM12878	blood:	n/a	chr17:38080867-38080876

No.	Distal block	Cell Line	Cell type
1	chr17:38080556..38082465-chr17:38135552..38137492,2	MCF-7	breast:
2	chr17:38080554..38082625-chr17:38096387..38098634,2	K562	blood:
3	chr17:38073834..38076577-chr17:38077829..38081795,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264968	TF binding region
ORMDL3	TF binding region
GSDMB	TF binding region
ENSG00000204913	Chromatin interaction
ENSG00000108344	Chromatin interaction
ENSG00000073605	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1453558	1.00[EUR][1000 genomes]
rs16965388	1.00[EUR][1000 genomes]
rs59246468	1.00[EUR][1000 genomes]
rs73985221	1.00[EUR][1000 genomes]
rs73985222	1.00[EUR][1000 genomes]
rs73985223	1.00[EUR][1000 genomes]
rs73985224	1.00[EUR][1000 genomes]
rs73985226	1.00[EUR][1000 genomes]
rs73985227	1.00[EUR][1000 genomes]
rs73985229	1.00[EUR][1000 genomes]
rs73985230	1.00[EUR][1000 genomes]
rs8071135	1.00[EUR][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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38059000-38082400	Weak transcription	Psoas Muscle	Psoas
2	chr17:38060400-38081600	Weak transcription	Fetal Brain Male	brain
3	chr17:38061800-38081000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:38073800-38081200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr17:38074200-38081000	Genic enhancers	Fetal Thymus	thymus
6	chr17:38074400-38082200	Genic enhancers	Placenta	Placenta
7	chr17:38074400-38082400	Weak transcription	Hela-S3	cervix
8	chr17:38075000-38081200	Strong transcription	Brain Germinal Matrix	brain
9	chr17:38075000-38081400	Genic enhancers	Fetal Intestine Large	intestine
10	chr17:38075200-38081000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:38075400-38081000	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr17:38075400-38081000	Strong transcription	Brain Cingulate Gyrus	brain
13	chr17:38075600-38081200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr17:38075600-38082200	Genic enhancers	Fetal Intestine Small	intestine
15	chr17:38076400-38081000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr17:38076600-38081000	Genic enhancers	Primary B cells from cord blood	blood
17	chr17:38076600-38082200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr17:38077200-38081000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr17:38077200-38082800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr17:38077800-38081000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr17:38078400-38081000	Weak transcription	Fetal Heart	heart
22	chr17:38079400-38082200	Weak transcription	HMEC	breast
23	chr17:38079800-38081200	Genic enhancers	Fetal Muscle Leg	muscle
24	chr17:38079800-38081600	Genic enhancers	Rectal Mucosa Donor 29	rectum
25	chr17:38079800-38082200	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr17:38080000-38081400	Genic enhancers	Thymus	Thymus
27	chr17:38080000-38081600	Weak transcription	Fetal Kidney	kidney
28	chr17:38080000-38082600	Flanking Active TSS	Liver	Liver
29	chr17:38080000-38083000	Weak transcription	Ovary	ovary
30	chr17:38080200-38081400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr17:38080200-38081400	Enhancers	HUVEC	blood vessel
32	chr17:38080200-38081600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr17:38080200-38081600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr17:38080200-38081600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:38080200-38081600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr17:38080200-38081600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr17:38080200-38081600	Genic enhancers	Esophagus	oesophagus
38	chr17:38080200-38081600	Genic enhancers	Pancreas	Pancrea
39	chr17:38080200-38082400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr17:38080200-38082400	Genic enhancers	Fetal Stomach	stomach
41	chr17:38080200-38082400	Enhancers	NH-A	brain
42	chr17:38080200-38082600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:38080200-38082800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr17:38080400-38081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:38080400-38081000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:38080400-38081000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr17:38080400-38081000	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr17:38080400-38081200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr17:38080400-38081200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr17:38080400-38081200	Weak transcription	K562	blood

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