Variant report

Variant	rs668750
Chromosome Location	chr15:41135827-41135828
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr15:41135827-41137451	GM12878	blood:	n/a	chr15:41136197-41136206 chr15:41136192-41136204 chr15:41135983-41135995
2	POLR2A	chr15:41135422-41137445	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr15:41135645-41137310	MCF-7	breast:	n/a	n/a
4	TAF1	chr15:41135745-41137209	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr15:41135393-41136741	MCF10A-Er-Src	breast:	n/a	n/a
6	SIN3AK20	chr15:41135661-41136335	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr15:41135442-41137369	HCT-116	colon:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
8	ZEB1	chr15:41135616-41136871	HepG2	liver:	n/a	chr15:41135832-41135843 chr15:41136372-41136379 chr15:41136370-41136379 chr15:41136646-41136657
9	ZBTB7A	chr15:41135746-41137301	ECC-1	luminal epithelium:	n/a	chr15:41136391-41136399
10	POLR2A	chr15:41135481-41137236	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr15:41135431-41136071	ECC-1	luminal epithelium:	n/a	n/a
12	MAX	chr15:41135464-41135997	ECC-1	luminal epithelium:	n/a	n/a
13	ZEB1	chr15:41135490-41137303	GM12878	blood:	n/a	chr15:41135832-41135843 chr15:41136372-41136379 chr15:41136370-41136379 chr15:41136646-41136657
14	E2F4	chr15:41135825-41135991	MCF10A-Er-Src	breast:	n/a	chr15:41135944-41135954 chr15:41135863-41135875 chr15:41135974-41135984
15	SIN3A	chr15:41135543-41137347	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr15:41135748-41136536	H1-hESC	embryonic stem cell:	n/a	chr15:41135944-41135957

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:41135793-41135843	PFSK-1	brain:	n/a
2	chr15:41135793-41135843	HEEpiC	esophagus:	n/a
3	chr15:41135793-41135843	SAEC	small airway:	n/a
4	chr15:41135793-41135843	NH-A	brain:	n/a
5	chr15:41135793-41135843	H1-hESC	embryonic stem cell:	embryo
6	chr15:41135793-41135843	GM12891	blood:	n/a
7	chr15:41135793-41135843	HRPEpiC	eye:	n/a
8	chr15:41135793-41135843	ProgFib	skin:	n/a
9	chr15:41135793-41135843	AG04449	skin:	fetal
10	chr15:41135793-41135843	PANC-1	pancreas:	n/a
11	chr15:41135793-41135843	GM12892	blood:	n/a
12	chr15:41135793-41135843	BJ	skin:	n/a
13	chr15:41135793-41135843	Jurkat	blood:	n/a
14	chr15:41135793-41135843	AG04450	lung:	fetal
15	chr15:41135793-41135843	HCF	heart:	n/a
16	chr15:41135793-41135843	RPTEC	kidney:	n/a
17	chr15:41135793-41135843	NHBE	bronchial:	n/a
18	chr15:41135793-41135843	CMK	blood:	n/a
19	chr15:41135793-41135843	HMEC	breast:	n/a
20	chr15:41135793-41135843	HPAEpiC	pulmonary alveolar:	n/a
21	chr15:41135793-41135843	A549	lung:	n/a
22	chr15:41135793-41135843	BE2_C	brain:	n/a
23	chr15:41135793-41135843	HNPCEpiC	eye:	n/a
24	chr15:41135793-41135843	GM06990	blood:	n/a
25	chr15:41135793-41135843	SK-N-MC	brain:	n/a
26	chr15:41135793-41135843	K562	blood:	n/a
27	chr15:41135793-41135843	Hepatocyte	liver:	n/a
28	chr15:41135793-41135843	HCPEpiC	choroid plexus:	n/a
29	chr15:41135793-41135843	Caco-2	colon:	n/a
30	chr15:41135793-41135843	GM12878	blood:	n/a
31	chr15:41135793-41135843	AoSMC	blood vessel:	n/a
32	chr15:41135793-41135843	GM19239	blood:	n/a
33	chr15:41135793-41135843	NHDF-neo	bronchial:	n/a
34	chr15:41135793-41135843	AG09319	gingival:	n/a
35	chr15:41135793-41135843	HL-60	blood:	n/a
36	chr15:41135793-41135843	MCF10A-Er-Src	breast:	n/a
37	chr15:41135793-41135843	HUVEC	blood vessel:	n/a
38	chr15:41135793-41135843	AG09309	skin:	n/a
39	chr15:41135793-41135843	ovcar-3	ovarian:	n/a
40	chr15:41135793-41135843	HIPEpiC	eye:	n/a
41	chr15:41135793-41135843	NB4	blood:	n/a
42	chr15:41135793-41135843	U87	brain:	n/a
43	chr15:41135793-41135843	SK-N-SH	brain:	n/a
44	chr15:41135793-41135843	SKMC	muscle:	n/a
45	chr15:41135793-41135843	HEK293	kidney:	embryo
46	chr15:41135793-41135843	HRE	kidney:	n/a
47	chr15:41135793-41135843	LNCaP	prostate:	n/a
48	chr15:41135793-41135843	HRCEpiC	kidney:	n/a
49	chr15:41135793-41135843	T-47D	breast:	n/a
50	chr15:41135793-41135843	HCT-116	colon:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41131767..41134219-chr15:41134403..41136032,2	MCF-7	breast:
2	chr15:41098435..41103357-chr15:41133527..41139132,10	MCF-7	breast:
3	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
4	chr15:41135781..41139367-chr15:41195514..41200270,4	MCF-7	breast:
5	chr15:41135079..41139908-chr15:41161283..41167324,7	MCF-7	breast:
6	chr15:41050847..41052798-chr15:41135268..41136987,2	K562	blood:
7	chr15:41120065..41123435-chr15:41135561..41137302,3	MCF-7	breast:
8	chr15:41099271..41102222-chr15:41135281..41137187,2	K562	blood:
9	chr15:41135632..41136132-chr6:117803609..117804174,2	HCT-116	colon:
10	chr15:41098123..41102222-chr15:41134582..41138137,4	K562	blood:
11	chr15:41135103..41140677-chr15:41182913..41189081,12	MCF-7	breast:
12	chr15:41129275..41132805-chr15:41134409..41137816,5	MCF-7	breast:
13	chr15:40985736..40987452-chr15:41134754..41137017,2	MCF-7	breast:
14	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261183	TF binding region
SPINT1	TF binding region
ENSG00000261183	CpG island
SPINT1	CpG island
ENSG00000104140	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000166143	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000164465	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000271236	Chromatin interaction
ENSG00000166140	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11639292	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2412569	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412570	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917953	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622538	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs668708	0.87[EUR][1000 genomes]
rs680493	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs689589	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689594	0.90[EUR][1000 genomes]
rs689618	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689733	0.85[EUR][1000 genomes]
rs689736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690435	0.90[EUR][1000 genomes]
rs690572	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690660	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs668750	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs668750	C15orf57	cis	Artery Tibial	GTEx
rs668750	RP11-111A22.1	cis	Artery Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41135200-41136000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:41135200-41136000	Flanking Active TSS	Fetal Intestine Small	intestine
3	chr15:41135200-41136000	Flanking Active TSS	Stomach Mucosa	stomach
4	chr15:41135200-41136000	Flanking Active TSS	HMEC	breast
5	chr15:41135200-41137800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr15:41135200-41138800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr15:41135200-41139000	Active TSS	Fetal Kidney	kidney
8	chr15:41135400-41136000	Flanking Active TSS	Placenta	Placenta
9	chr15:41135400-41137000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr15:41135400-41137000	Active TSS	Duodenum Mucosa	Duodenum
11	chr15:41135400-41137400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:41135400-41137600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:41135600-41136000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:41135600-41136000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:41135600-41136000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:41135600-41136000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
17	chr15:41135600-41136000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
18	chr15:41135600-41136000	Flanking Active TSS	Pancreas	Pancrea
19	chr15:41135600-41136000	Flanking Active TSS	K562	blood
20	chr15:41135600-41136200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:41135600-41136200	Enhancers	Liver	Liver
22	chr15:41135600-41136200	Bivalent Enhancer	Brain Substantia Nigra	brain
23	chr15:41135600-41136200	Enhancers	Spleen	Spleen
24	chr15:41135600-41136800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:41135600-41136800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
26	chr15:41135600-41137200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr15:41135600-41137200	Flanking Active TSS	Colonic Mucosa	Colon
28	chr15:41135600-41137200	Active TSS	Small Intestine	intestine
29	chr15:41135600-41137400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr15:41135600-41137400	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:41135600-41137400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr15:41135600-41137600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr15:41135600-41137600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:41135600-41137600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
35	chr15:41135600-41137600	Active TSS	Placenta Amnion	Placenta Amnion
36	chr15:41135600-41138200	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr15:41135600-41138400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr15:41135600-41138400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:41135600-41138600	Active TSS	Gastric	stomach
40	chr15:41135600-41140200	Active TSS	Rectal Smooth Muscle	rectum
41	chr15:41135600-41140400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:41135800-41136000	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr15:41135800-41136000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
44	chr15:41135800-41136000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
45	chr15:41135800-41136000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr15:41135800-41136000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:41135800-41136000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
48	chr15:41135800-41136000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:41135800-41136000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
50	chr15:41135800-41136000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain

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