Variant report

Variant	rs12150518
Chromosome Location	chr17:15406197-15406198
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:161)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:161 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:15405925-15406653	HCT-116	colon:	n/a	n/a
2	POLR2A	chr17:15406129-15406753	K562	blood:	n/a	n/a
3	YY1	chr17:15406162-15406395	K562	blood:	n/a	n/a
4	CTCF	chr17:15405955-15406522	IMR90	lung:	n/a	n/a
5	CTCF	chr17:15406051-15406423	HepG2	liver:	n/a	n/a
6	RAD21	chr17:15406074-15406489	A549	lung:	n/a	n/a
7	CTCF	chr17:15405997-15406555	K562	blood:	n/a	n/a
8	RAD21	chr17:15406013-15406500	SK-N-SH_RA	brain:	n/a	n/a
9	YY1	chr17:15406090-15406469	SK-N-SH_RA	brain:	n/a	n/a
10	CTCF	chr17:15406141-15406634	HCT-116	colon:	n/a	n/a
11	MAX	chr17:15406065-15406430	SK-N-SH	brain:	n/a	n/a
12	PML	chr17:15406008-15406444	GM12878	blood:	n/a	n/a
13	CTCF	chr17:15406163-15406467	GM19238	blood:	n/a	n/a
14	SMC3	chr17:15406039-15406481	GM12878	blood:	n/a	n/a
15	RAD21	chr17:15406007-15406603	SK-N-SH_RA	brain:	n/a	n/a
16	POLR2A	chr17:15406131-15406503	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr17:15406078-15406515	H1-hESC	embryonic stem cell:	n/a	n/a
18	SPI1	chr17:15406146-15406273	K562	blood:	n/a	n/a
19	CTCF	chr17:15406089-15406720	GM12878	blood:	n/a	n/a
20	RAD21	chr17:15406133-15406413	K562	blood:	n/a	n/a
21	CTCF	chr17:15406180-15406422	ProgFib	skin:	n/a	n/a
22	CTCF	chr17:15406080-15406230	A549	lung:	n/a	n/a
23	SMC3	chr17:15405812-15406689	SK-N-SH	brain:	n/a	n/a
24	RAD21	chr17:15406028-15406549	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr17:15406164-15406448	LNCaP	prostate:	n/a	n/a
26	RAD21	chr17:15406109-15406509	Hela-S3	cervix:	n/a	n/a
27	RAD21	chr17:15406093-15406509	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr17:15406120-15406270	HFF-Myc	foreskin:	n/a	n/a
29	MAX	chr17:15406071-15406730	A549	lung:	n/a	n/a
30	CTCF	chr17:15406175-15406381	SK-N-SH_RA	brain:	n/a	n/a
31	CTCF	chr17:15406172-15406445	Lung_OC	lung:	n/a	n/a
32	CTCF	chr17:15406121-15406377	ECC-1	luminal epithelium:	n/a	n/a
33	ZNF143	chr17:15406085-15406447	K562	blood:	n/a	n/a
34	SPI1	chr17:15406088-15406362	GM12891	blood:	n/a	n/a
35	RAD21	chr17:15405970-15406622	MCF-7	breast:	n/a	n/a
36	CTCF	chr17:15406194-15406432	K562	blood:	n/a	n/a
37	CTCF	chr17:15406196-15406437	MCF-7	breast:	n/a	n/a
38	POLR2A	chr17:15405279-15408288	K562	blood:	n/a	n/a
39	STAT3	chr17:15406193-15406546	MCF10A-Er-Src	breast:	n/a	n/a
40	CTCF	chr17:15406178-15406449	MCF-7	breast:	n/a	n/a
41	CREB1	chr17:15406090-15406528	A549	lung:	n/a	n/a
42	EP300	chr17:15406128-15406427	GM12878	blood:	n/a	n/a
43	RAD21	chr17:15406094-15406460	HepG2	liver:	n/a	n/a
44	PML	chr17:15406132-15406530	MCF-7	breast:	n/a	n/a
45	E2F6	chr17:15406140-15406781	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr17:15406166-15406486	Spleen_OC	spleen:	n/a	n/a
47	RAD21	chr17:15406100-15406468	H1-hESC	embryonic stem cell:	n/a	n/a
48	MAZ	chr17:15406115-15406461	K562	blood:	n/a	n/a
49	SMC3	chr17:15406090-15406508	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr17:15406179-15406462	GM12892	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:15164289..15164844-chr17:15406132..15406721,2	K562	blood:
2	chr17:15160379..15161319-chr17:15405087..15406751,8	MCF-7	breast:
3	chr17:15165016..15165581-chr17:15405777..15406684,2	MCF-7	breast:
4	chr17:15163427..15164223-chr17:15405796..15406340,2	K562	blood:
5	chr17:15163915..15164727-chr17:15406027..15406796,2	MCF-7	breast:
6	chr17:15398558..15401467-chr17:15403715..15406504,4	K562	blood:
7	chr17:15339768..15340717-chr17:15405925..15406718,2	K562	blood:
8	chr17:15151336..15152140-chr17:15405875..15406419,3	MCF-7	breast:
9	chr17:15160307..15161319-chr17:15405440..15406372,3	MCF-7	breast:
10	chr17:15398558..15401467-chr17:15404011..15406504,2	K562	blood:
11	chr17:15162964..15164800-chr17:15405391..15407046,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223878	TF binding region
ENSG00000265445	Chromatin interaction
ENSG00000109099	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12150334	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2954790	1.00[YRI][hapmap]
rs4792617	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57926686	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58269369	0.86[ASN][1000 genomes]
rs72819828	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72824466	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72824474	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72824475	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72824478	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72824479	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72824480	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72824487	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72824491	0.96[EUR][1000 genomes]
rs72824493	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72824496	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72824497	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12150518	AC005517.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12150518	CDRT4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15377400-15406400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr17:15383200-15419600	Weak transcription	Thymus	Thymus
3	chr17:15383400-15455000	Weak transcription	Gastric	stomach
4	chr17:15384600-15406200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:15385600-15418000	Weak transcription	Pancreas	Pancrea
6	chr17:15387200-15417000	Weak transcription	Small Intestine	intestine
7	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr17:15394600-15406400	Weak transcription	Stomach Mucosa	stomach
9	chr17:15394600-15417000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:15395000-15410200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:15395400-15413400	Weak transcription	Hela-S3	cervix
13	chr17:15396000-15417200	Weak transcription	Fetal Brain Male	brain
14	chr17:15396800-15420400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr17:15398000-15406200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:15398800-15406200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr17:15398800-15408800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr17:15399000-15408800	Strong transcription	HepG2	liver
19	chr17:15400800-15413000	Weak transcription	NH-A	brain
20	chr17:15401200-15420400	Weak transcription	Psoas Muscle	Psoas
21	chr17:15402800-15410200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:15403000-15410200	Weak transcription	Fetal Brain Female	brain
23	chr17:15404600-15406400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:15404600-15406800	Enhancers	Fetal Kidney	kidney
25	chr17:15404600-15406800	Enhancers	HUVEC	blood vessel
26	chr17:15405000-15406200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr17:15405000-15406800	Enhancers	Esophagus	oesophagus
28	chr17:15405000-15406800	Enhancers	Spleen	Spleen
29	chr17:15405200-15406200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr17:15405200-15406200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr17:15405200-15406200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr17:15405200-15406600	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr17:15405200-15406800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:15405400-15406200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr17:15405400-15406200	Active TSS	Colonic Mucosa	Colon
36	chr17:15405400-15406400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr17:15405400-15406600	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr17:15405400-15406600	Enhancers	Fetal Heart	heart
39	chr17:15405400-15406800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:15405400-15410200	Weak transcription	Primary T cells from cord blood	blood
41	chr17:15405400-15418200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr17:15405400-15419000	Weak transcription	Liver	Liver
43	chr17:15405600-15406200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:15405600-15406200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr17:15405600-15406200	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr17:15405600-15406200	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr17:15405600-15406200	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr17:15405600-15406200	Flanking Active TSS	Fetal Muscle Trunk	muscle
49	chr17:15405600-15406200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr17:15405600-15406200	Flanking Active TSS	NHDF-Ad	bronchial

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