Variant report

Variant	rs7502233
Chromosome Location	chr17:38218804-38218805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:38218740-38218890	HPF	lung:	n/a	n/a
2	EGR1	chr17:38218796-38219329	K562	blood:	n/a	chr17:38219129-38219143 chr17:38219128-38219141
3	CTCF	chr17:38218700-38218850	NHEK	skin:	n/a	n/a
4	MAZ	chr17:38218701-38219905	HepG2	liver:	n/a	n/a
5	CTCF	chr17:38218800-38218950	HAc	cerebellar:	n/a	n/a
6	ZBTB7A	chr17:38218158-38219960	K562	blood:	n/a	chr17:38218854-38218868
7	CTCF	chr17:38218700-38218850	RPTEC	kidney:	n/a	n/a
8	RAD21	chr17:38218525-38220199	SK-N-SH	brain:	n/a	chr17:38219783-38219796 chr17:38219720-38219733 chr17:38219796-38219808
9	CTCF	chr17:38218780-38218930	NHDF-neo	bronchial:	n/a	n/a
10	MYBL2	chr17:38218452-38218924	HepG2	liver:	n/a	n/a
11	CTCF	chr17:38218760-38218910	GM12870	blood:	n/a	n/a
12	CTCF	chr17:38218790-38218861	GM12891	blood:	n/a	n/a
13	CTCF	chr17:38218740-38218890	AG09309	skin:	n/a	n/a
14	ZBTB7A	chr17:38218572-38219980	K562	blood:	n/a	chr17:38218854-38218868
15	CTCF	chr17:38218660-38218810	GM12868	blood:	n/a	n/a
16	CTCF	chr17:38218760-38218910	HMF	breast:	n/a	n/a
17	CTCF	chr17:38218740-38218890	GM12872	blood:	n/a	n/a
18	CTCF	chr17:38218700-38218850	HPAF	blood vessel:	n/a	n/a
19	ZBTB7A	chr17:38218683-38220292	ECC-1	luminal epithelium:	n/a	chr17:38218854-38218868
20	CTCF	chr17:38218700-38218850	HEK293	kidney:	n/a	n/a
21	CTCF	chr17:38218800-38218950	HRPEpiC	eye:	n/a	n/a
22	MAZ	chr17:38218664-38219857	GM12878	blood:	n/a	n/a
23	CTCF	chr17:38218680-38218830	HBMEC	blood vessel:	n/a	n/a
24	CTCF	chr17:38218740-38218890	HepG2	liver:	n/a	n/a
25	CTCF	chr17:38218720-38218870	K562	blood:	n/a	n/a
26	MXI1	chr17:38218480-38222365	SK-N-SH	brain:	n/a	n/a
27	CTCF	chr17:38218768-38218863	GM12892	blood:	n/a	n/a
28	CTCF	chr17:38218740-38218890	GM12873	blood:	n/a	n/a
29	MAX	chr17:38218501-38218807	K562	blood:	n/a	n/a
30	CTCF	chr17:38218660-38218810	GM12864	blood:	n/a	n/a
31	CTCF	chr17:38218720-38218870	HCPEpiC	choroid plexus:	n/a	n/a
32	CTCF	chr17:38218800-38218950	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr17:38218720-38218870	AG09319	gingival:	n/a	n/a
34	CTCF	chr17:38218700-38218850	GM12871	blood:	n/a	n/a
35	RCOR1	chr17:38218598-38218862	K562	blood:	n/a	n/a
36	MYC	chr17:38218736-38218879	HepG2	liver:	n/a	n/a
37	RCOR1	chr17:38218610-38218828	HepG2	liver:	n/a	n/a
38	CTCF	chr17:38218740-38218890	HPAF	blood vessel:	n/a	n/a
39	SIN3A	chr17:38218544-38218867	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr17:38218747-38218850	GM12878	blood:	n/a	n/a
41	CTCF	chr17:38218740-38218890	AoAF	blood vessel:	n/a	n/a
42	YY1	chr17:38218594-38219939	HepG2	liver:	n/a	chr17:38219728-38219742 chr17:38219734-38219745 chr17:38219154-38219168 chr17:38219128-38219139 chr17:38219154-38219163
43	CTCF	chr17:38218720-38218870	HA-sp	spinal cord:	n/a	n/a
44	JUND	chr17:38218770-38218818	H1-hESC	embryonic stem cell:	n/a	n/a
45	ZBTB7A	chr17:38218629-38220247	ECC-1	luminal epithelium:	n/a	chr17:38218854-38218868
46	CTCF	chr17:38218700-38218850	GM12873	blood:	n/a	n/a
47	CTCF	chr17:38218737-38218895	GM19240	blood:	n/a	n/a
48	BHLHE40	chr17:38218514-38218813	K562	blood:	n/a	n/a
49	CTCF	chr17:38218745-38218848	GM19239	blood:	n/a	n/a
50	MAZ	chr17:38218571-38220427	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:38218791-38218841	HL-60	blood:	n/a
2	chr17:38218791-38218841	HUVEC	blood vessel:	n/a
3	chr17:38218791-38218841	RPTEC	kidney:	n/a
4	chr17:38218791-38218841	SK-N-MC	brain:	n/a
5	chr17:38218791-38218841	MCF10A-Er-Src	breast:	n/a
6	chr17:38218791-38218841	ECC-1	luminal epithelium:	n/a
7	chr17:38218791-38218841	BJ	skin:	n/a
8	chr17:38218791-38218841	HEK293	kidney:	embryo
9	chr17:38218791-38218841	IMR90	lung:	fetal
10	chr17:38218791-38218841	BE2_C	brain:	n/a
11	chr17:38218791-38218841	SK-N-SH_RA	brain:	n/a
12	chr17:38218791-38218841	NHDF-neo	bronchial:	n/a
13	chr17:38218791-38218841	Caco-2	colon:	n/a
14	chr17:38218791-38218841	A549	lung:	n/a
15	chr17:38218791-38218841	AG10803	skin:	n/a
16	chr17:38218791-38218841	AG04450	lung:	fetal
17	chr17:38218791-38218841	PFSK-1	brain:	n/a
18	chr17:38218791-38218841	HepG2	liver:	n/a
19	chr17:38218791-38218841	AG09309	skin:	n/a
20	chr17:38218791-38218841	SKMC	muscle:	n/a
21	chr17:38218791-38218841	ProgFib	skin:	n/a
22	chr17:38218791-38218841	PrEC	prostate:	n/a
23	chr17:38218791-38218841	HPAEpiC	pulmonary alveolar:	n/a
24	chr17:38218791-38218841	HCF	heart:	n/a
25	chr17:38218791-38218841	U87	brain:	n/a
26	chr17:38218791-38218841	LNCaP	prostate:	n/a
27	chr17:38218791-38218841	SK-N-SH	brain:	n/a
28	chr17:38218791-38218841	K562	blood:	n/a
29	chr17:38218791-38218841	CMK	blood:	n/a
30	chr17:38218791-38218841	HNPCEpiC	eye:	n/a
31	chr17:38218791-38218841	PANC-1	pancreas:	n/a
32	chr17:38218791-38218841	HCPEpiC	choroid plexus:	n/a
33	chr17:38218791-38218841	GM19239	blood:	n/a
34	chr17:38218791-38218841	HRPEpiC	eye:	n/a
35	chr17:38218791-38218841	HCM	heart:	n/a
36	chr17:38218791-38218841	GM12892	blood:	n/a
37	chr17:38218791-38218841	HRE	kidney:	n/a
38	chr17:38218791-38218841	NHBE	bronchial:	n/a
39	chr17:38218791-38218841	MCF-7	breast:	n/a
40	chr17:38218791-38218841	Jurkat	blood:	n/a
41	chr17:38218791-38218841	AoSMC	blood vessel:	n/a
42	chr17:38218791-38218841	SAEC	small airway:	n/a
43	chr17:38218791-38218841	HAEpiC	amniotic membrane:	n/a
44	chr17:38218791-38218841	GM06990	blood:	n/a
45	chr17:38218791-38218841	AG04449	skin:	fetal
46	chr17:38218791-38218841	NT2-D1	testis:	n/a
47	chr17:38218791-38218841	HCT-116	colon:	n/a
48	chr17:38218791-38218841	HEEpiC	esophagus:	n/a
49	chr17:38218791-38218841	HRCEpiC	kidney:	n/a
50	chr17:38218791-38218841	GM12878	blood:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38218382..38219065-chr17:38324572..38325105,2	MCF-7	breast:
2	chr17:38218404..38220452-chr17:38276626..38279762,4	K562	blood:
3	chr17:38218404..38220452-chr17:38276626..38279762,3	K562	blood:
4	chr17:38216131..38218859-chr17:38295458..38297078,2	K562	blood:
5	chr17:38210481..38212413-chr17:38218576..38220480,2	MCF-7	breast:
6	chr17:38181477..38183501-chr17:38217583..38219827,2	MCF-7	breast:
7	chr17:38216722..38220271-chr17:38254476..38257952,5	K562	blood:
8	chr17:38217616..38219835-chr17:38296248..38299363,4	K562	blood:

No data

Variant related genes	Relation type
MED24	TF binding region
THRA	TF binding region
THRA	CpG island
MED24	CpG island
ENSG00000108349	Chromatin interaction
ENSG00000126368	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000008838	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11078936	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs12601929	0.81[GIH][hapmap];0.88[MEX][hapmap]
rs34670005	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7502539	0.87[AMR][1000 genomes];0.91[EUR][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	nsv908221	chr17:38216522-38289003	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	esv3393448	chr17:38218451-38220999	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7502233	KRT222	cis	cerebellum	SCAN
rs7502233	PCGF2	cis	cerebellum	SCAN
rs7502233	PSMD3	cis	parietal	SCAN
rs7502233	MED24	cis	cerebellum	SCAN
rs7502233	KRT23	cis	parietal	SCAN
rs7502233	CCL2	cis	cerebellum	SCAN
rs7502233	MED24	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38218000-38219000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr17:38218400-38219000	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr17:38218400-38219000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr17:38218400-38219000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr17:38218400-38219000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr17:38218400-38219000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr17:38218400-38219000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr17:38218400-38219000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr17:38218400-38219000	Flanking Active TSS	Fetal Muscle Trunk	muscle
10	chr17:38218400-38219000	Enhancers	Lung	lung
11	chr17:38218400-38219000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr17:38218400-38219000	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr17:38218400-38219000	Flanking Active TSS	Dnd41	blood
14	chr17:38218400-38219000	Flanking Active TSS	Hela-S3	cervix
15	chr17:38218400-38219000	Flanking Active TSS	K562	blood
16	chr17:38218400-38220200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:38218400-38220200	Active TSS	Brain Substantia Nigra	brain
18	chr17:38218400-38220400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr17:38218400-38220800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr17:38218600-38219000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:38218600-38219000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:38218600-38219000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr17:38218600-38219000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr17:38218600-38219000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr17:38218600-38219000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr17:38218600-38219000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:38218600-38219000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:38218600-38219000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr17:38218600-38219000	Flanking Active TSS	Liver	Liver
30	chr17:38218600-38219000	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr17:38218600-38219000	Flanking Active TSS	Placenta	Placenta
32	chr17:38218600-38219000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
33	chr17:38218600-38219000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr17:38218600-38219000	Flanking Active TSS	Thymus	Thymus
35	chr17:38218600-38219000	Flanking Active TSS	HUVEC	blood vessel
36	chr17:38218600-38219000	Flanking Active TSS	NHLF	lung
37	chr17:38218600-38219000	Flanking Active TSS	Osteobl	bone
38	chr17:38218600-38219200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr17:38218600-38219800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr17:38218600-38219800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:38218600-38219800	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr17:38218600-38219800	Active TSS	Colonic Mucosa	Colon
43	chr17:38218600-38219800	Active TSS	HSMM	muscle
44	chr17:38218600-38220000	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr17:38218600-38220000	Active TSS	Right Ventricle	heart
46	chr17:38218600-38220200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
47	chr17:38218600-38220200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr17:38218600-38220200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr17:38218600-38220200	Active TSS	Psoas Muscle	Psoas
50	chr17:38218600-38220400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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