Variant report

Variant	rs11631193
Chromosome Location	chr15:42867390-42867391
allele	C/G
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	POLR2A	chr15:42867167-42868154	ProgFib	skin:	n/a	n/a
2	E2F6	chr15:42867132-42868315	A549	lung:	n/a	chr15:42867462-42867473 chr15:42867463-42867475 chr15:42867769-42867779 chr15:42867697-42867706 chr15:42867714-42867726 chr15:42867302-42867312 chr15:42867584-42867596 chr15:42867817-42867826
3	BRCA1	chr15:42867171-42867861	Hela-S3	cervix:	n/a	n/a
4	NFIC	chr15:42867330-42868546	ECC-1	luminal epithelium:	n/a	n/a
5	SETDB1	chr15:42866992-42867533	U2OS	brain:	n/a	n/a
6	BHLHE40	chr15:42867233-42867556	A549	lung:	n/a	n/a
7	POLR2A	chr15:42867378-42867993	MCF-7	breast:	n/a	n/a
8	JUND	chr15:42867096-42867944	K562	blood:	n/a	chr15:42867696-42867705 chr15:42867816-42867825
9	POLR2A	chr15:42867102-42868182	GM12892	blood:	n/a	n/a
10	NFYA	chr15:42867291-42867884	Hela-S3	cervix:	n/a	n/a
11	RFX5	chr15:42867129-42867887	Hela-S3	cervix:	n/a	chr15:42867209-42867222
12	POLR2A	chr15:42867332-42868307	IMR90	lung:	n/a	n/a
13	MAX	chr15:42866909-42868453	ECC-1	luminal epithelium:	n/a	chr15:42867809-42867818
14	CTCF	chr15:42867300-42867450	GM12869	blood:	n/a	n/a
15	MAX	chr15:42867141-42868356	K562	blood:	n/a	chr15:42867809-42867818
16	TCF7L2	chr15:42867348-42868229	HCT-116	colon:	n/a	n/a
17	EP300	chr15:42867187-42867720	HepG2	liver:	n/a	n/a
18	POLR2A	chr15:42867214-42867783	K562	blood:	n/a	n/a
19	IRF1	chr15:42867270-42867976	K562	blood:	n/a	chr15:42867696-42867710 chr15:42867753-42867767 chr15:42867440-42867454
20	MAX	chr15:42867025-42868423	SK-N-SH	brain:	n/a	chr15:42867809-42867818
21	ZKSCAN1	chr15:42867384-42867754	Hela-S3	cervix:	n/a	n/a
22	PAX5	chr15:42867204-42867848	GM12878	blood:	n/a	chr15:42867434-42867453
23	MAX	chr15:42867113-42868030	MCF-7	breast:	n/a	chr15:42867809-42867818
24	TAF1	chr15:42867266-42868309	HepG2	liver:	n/a	n/a
25	MAX	chr15:42867055-42868579	HepG2	liver:	n/a	chr15:42867809-42867818
26	BHLHE40	chr15:42867126-42868327	K562	blood:	n/a	chr15:42867776-42867792 chr15:42867765-42867781
27	MYC	chr15:42867122-42868128	A549	lung:	n/a	chr15:42867809-42867818
28	RCOR1	chr15:42867351-42868075	GM12878	blood:	n/a	n/a
29	MYC	chr15:42867390-42867392	MCF-7	breast:	n/a	n/a
30	E2F6	chr15:42866979-42868526	A549	lung:	n/a	chr15:42867462-42867473 chr15:42867463-42867475 chr15:42867769-42867779 chr15:42867697-42867706 chr15:42867714-42867726 chr15:42867302-42867312 chr15:42867584-42867596 chr15:42867817-42867826
31	CCNT2	chr15:42867230-42868278	K562	blood:	n/a	chr15:42868077-42868086
32	TAF1	chr15:42867300-42867996	Hela-S3	cervix:	n/a	n/a
33	MAX	chr15:42867041-42868436	ECC-1	luminal epithelium:	n/a	chr15:42867809-42867818
34	SP1	chr15:42867162-42868005	HepG2	liver:	n/a	chr15:42867561-42867572 chr15:42867528-42867537 chr15:42867437-42867451 chr15:42867818-42867827 chr15:42867698-42867707 chr15:42867823-42867832 chr15:42867696-42867708 chr15:42867816-42867828 chr15:42867442-42867451 chr15:42867657-42867666 chr15:42867440-42867452 chr15:42867816-42867828 chr15:42867697-42867706 chr15:42867693-42867707 chr15:42867696-42867708
35	HEY1	chr15:42867132-42868054	HepG2	liver:	n/a	chr15:42867761-42867776 chr15:42867779-42867794
36	MXI1	chr15:42866252-42869441	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr15:42867295-42868039	GM12891	blood:	n/a	n/a
38	POLR2A	chr15:42867238-42868079	K562	blood:	n/a	n/a
39	POLR2A	chr15:42867168-42868024	HepG2	liver:	n/a	n/a
40	POLR2A	chr15:42867108-42868165	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr15:42867002-42868493	SK-N-MC	brain:	n/a	n/a
42	POLR2A	chr15:42867257-42868002	A549	lung:	n/a	n/a
43	TAF1	chr15:42867259-42868048	SK-N-SH	brain:	n/a	n/a
44	MAX	chr15:42867058-42868069	SK-N-SH	brain:	n/a	chr15:42867809-42867818
45	MAFK	chr15:42867277-42867780	Hela-S3	cervix:	n/a	n/a
46	MAX	chr15:42867065-42868623	H1-hESC	embryonic stem cell:	n/a	chr15:42867809-42867818
47	EP300	chr15:42867307-42867742	GM12878	blood:	n/a	n/a
48	TEAD4	chr15:42867225-42867805	ECC-1	luminal epithelium:	n/a	n/a
49	TBP	chr15:42867174-42868543	K562	blood:	n/a	n/a
50	USF1	chr15:42867315-42867939	SK-N-SH_RA	brain:	n/a	chr15:42867776-42867792 chr15:42867765-42867781

No.	Distal block	Cell Line	Cell type
1	chr11:71791137..71792001-chr15:42866964..42867628,2	Hela-S3	cervix:
2	chr15:42866660..42868750-chr15:42872207..42873779,2	K562	blood:
3	chr15:42838345..42842657-chr15:42865696..42868936,4	MCF-7	breast:
4	chr15:42840104..42842482-chr15:42865653..42867827,2	K562	blood:
5	chr15:42862243..42864590-chr15:42865875..42867418,2	K562	blood:
6	chr15:42866281..42869584-chr15:42871180..42873707,4	K562	blood:
7	chr15:42838709..42841070-chr15:42866779..42868984,2	MCF-7	breast:
8	chr15:42783274..42784836-chr15:42864927..42867645,2	K562	blood:
9	chr15:42840090..42842755-chr15:42865653..42870684,5	K562	blood:
10	chr15:42854171..42864590-chr15:42864872..42869799,12	K562	blood:
11	chr15:42801179..42804150-chr15:42867351..42869271,2	K562	blood:
12	chr15:42785710..42787693-chr15:42866156..42868186,2	K562	blood:

Variant related genes	Relation type
STARD9	TF binding region
ENSG00000137814	Chromatin interaction
ENSG00000180979	Chromatin interaction
ENSG00000103994	Chromatin interaction
ENSG00000261822	Chromatin interaction
ENSG00000260282	Chromatin interaction
ENSG00000092531	Chromatin interaction
ENSG00000184154	Chromatin interaction
ENSG00000260490	Chromatin interaction
ENSG00000137497	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10454039	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1060291	0.88[EUR][1000 genomes]
rs10851410	0.93[EUR][1000 genomes]
rs10851411	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11022	0.88[EUR][1000 genomes]
rs11070374	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11632169	0.83[ASN][1000 genomes]
rs11638208	0.81[EUR][1000 genomes]
rs1197546	0.83[ASN][1000 genomes]
rs1197547	0.84[ASN][1000 genomes]
rs1211642	0.84[ASN][1000 genomes]
rs12324113	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12324717	0.94[EUR][1000 genomes]
rs12903416	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12903432	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12906697	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1667493	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1705360	0.86[ASN][1000 genomes]
rs1814518	0.88[ASN][1000 genomes]
rs1900921	0.88[EUR][1000 genomes]
rs2241998	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255995	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2595939	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2595940	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2595941	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2617236	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2899051	0.83[EUR][1000 genomes]
rs2899057	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34643746	0.94[EUR][1000 genomes]
rs3986280	0.94[EUR][1000 genomes]
rs4447398	0.84[ASN][1000 genomes]
rs4573906	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4923948	0.87[EUR][1000 genomes]
rs4924684	0.88[EUR][1000 genomes]
rs56357092	0.88[EUR][1000 genomes]
rs60380503	0.87[EUR][1000 genomes]
rs6493053	0.81[AMR][1000 genomes]
rs6493054	0.86[ASN][1000 genomes]
rs7168835	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8033412	0.88[EUR][1000 genomes]
rs876992	0.88[ASN][1000 genomes]
rs9302112	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9783683	0.84[AMR][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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv976927	chr15:42862948-42868443	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11631193	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx
rs11631193	CEP27	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42842600-42867400	Weak transcription	Small Intestine	intestine
2	chr15:42855200-42867800	Weak transcription	Aorta	Aorta
3	chr15:42859000-42868000	Weak transcription	Fetal Brain Male	brain
4	chr15:42859400-42867800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:42859600-42867400	Weak transcription	Gastric	stomach
6	chr15:42860400-42867800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:42866400-42867400	Flanking Active TSS	K562	blood
8	chr15:42866600-42867400	Enhancers	Fetal Heart	heart
9	chr15:42866800-42867400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:42866800-42867400	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr15:42866800-42867400	Flanking Active TSS	Fetal Intestine Small	intestine
12	chr15:42866800-42867400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr15:42866800-42868000	Active TSS	Brain Germinal Matrix	brain
14	chr15:42867000-42867400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:42867000-42867400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr15:42867000-42867400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr15:42867000-42867400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
18	chr15:42867000-42867400	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr15:42867000-42867400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr15:42867000-42867400	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr15:42867000-42867400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr15:42867000-42867400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr15:42867000-42867400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:42867000-42867400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr15:42867000-42867400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:42867000-42867400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr15:42867000-42867400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:42867000-42867400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:42867000-42867400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr15:42867000-42867400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr15:42867000-42867400	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr15:42867000-42867400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:42867000-42867400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr15:42867000-42867400	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr15:42867000-42867400	Flanking Active TSS	Fetal Muscle Trunk	muscle
36	chr15:42867000-42867400	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr15:42867000-42867400	Flanking Active TSS	Placenta	Placenta
38	chr15:42867000-42867400	Flanking Active TSS	Fetal Stomach	stomach
39	chr15:42867000-42867400	Flanking Active TSS	Fetal Thymus	thymus
40	chr15:42867000-42867400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr15:42867000-42867400	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr15:42867000-42867400	Flanking Active TSS	Thymus	Thymus
43	chr15:42867000-42867400	Flanking Active TSS	GM12878-XiMat	blood
44	chr15:42867000-42867400	Flanking Active TSS	Hela-S3	cervix
45	chr15:42867000-42867400	Flanking Active TSS	HepG2	liver
46	chr15:42867000-42867400	Flanking Active TSS	HMEC	breast
47	chr15:42867000-42867400	Flanking Active TSS	HSMM	muscle
48	chr15:42867000-42867400	Flanking Active TSS	HUVEC	blood vessel
49	chr15:42867000-42867400	Flanking Active TSS	NH-A	brain
50	chr15:42867000-42867600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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