Variant report

Variant	rs9567983
Chromosome Location	chr13:48613069-48613070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr13:48612987-48613195	GM12878	blood:	n/a	n/a
2	PBX3	chr13:48611414-48613130	SK-N-SH	brain:	n/a	n/a
3	RFX5	chr13:48612664-48613158	GM12878	blood:	n/a	n/a
4	POLR2A	chr13:48612824-48613199	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr13:48613044-48613095	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr13:48611391-48613186	GM12878	blood:	n/a	n/a
7	POLR2A	chr13:48613010-48613252	K562	blood:	n/a	n/a
8	POLR2A	chr13:48612982-48613707	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBL1XR1	chr13:48612795-48613184	GM12878	blood:	n/a	n/a
10	SPI1	chr13:48612891-48613124	GM12878	blood:	n/a	n/a
11	MXI1	chr13:48610981-48613175	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr13:48611355-48613599	K562	blood:	n/a	n/a
13	POLR2A	chr13:48611141-48613548	SK-N-MC	brain:	n/a	n/a
14	WRNIP1	chr13:48613026-48613517	GM12878	blood:	n/a	n/a
15	RCOR1	chr13:48613033-48613304	K562	blood:	n/a	n/a
16	POLR2A	chr13:48612964-48613361	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr13:48611263-48613590	GM12891	blood:	n/a	n/a
18	POLR2A	chr13:48611253-48613185	Raji	blood:	n/a	n/a
19	MAZ	chr13:48612922-48613122	GM12878	blood:	n/a	n/a
20	EBF1	chr13:48613032-48613279	GM12878	blood:	n/a	n/a
21	POLR2A	chr13:48612927-48613574	H1-hESC	embryonic stem cell:	n/a	n/a
22	CUX1	chr13:48611444-48613131	GM12878	blood:	n/a	n/a
23	POLR2A	chr13:48611194-48613506	GM12878	blood:	n/a	n/a
24	POLR2A	chr13:48611261-48613291	HepG2	liver:	n/a	n/a
25	POLR2A	chr13:48613040-48613107	ProgFib	skin:	n/a	n/a
26	MAZ	chr13:48611288-48613261	IMR90	lung:	n/a	n/a
27	POLR2A	chr13:48611243-48613310	IMR90	lung:	n/a	n/a
28	IKZF1	chr13:48612916-48613164	GM12878	blood:	n/a	n/a
29	POLR2A	chr13:48610990-48613373	GM12878	blood:	n/a	n/a
30	POLR2A	chr13:48613052-48613076	MCF-7	breast:	n/a	n/a
31	RCOR1	chr13:48611522-48613255	GM12878	blood:	n/a	n/a
32	POLR2A	chr13:48612961-48613339	GM12891	blood:	n/a	n/a
33	EP300	chr13:48612712-48613283	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr13:48573666..48577274-chr13:48610467..48613685,4	MCF-7	breast:
2	chr13:48612235..48613841-chr13:48623262..48624820,2	K562	blood:
3	chr13:48610643..48613395-chr13:48668732..48670612,2	MCF-7	breast:
4	chr13:48611688..48613332-chr7:101457559..101460225,2	MCF-7	breast:
5	chr13:48612252..48613991-chr13:48614134..48616270,2	MCF-7	breast:
6	chr13:48573863..48576384-chr13:48611584..48613293,2	K562	blood:
7	chr13:48612381..48615273-chr13:48617254..48619078,2	MCF-7	breast:
8	chr13:48612019..48613651-chr13:48806032..48808331,2	MCF-7	breast:

No data

Variant related genes	Relation type
SUCLA2	TF binding region
ENSG00000136143	Chromatin interaction
ENSG00000136146	Chromatin interaction
ENSG00000227848	Chromatin interaction
ENSG00000136156	Chromatin interaction
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11617143	0.80[EUR][1000 genomes]
rs11617714	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11618304	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11618554	0.80[EUR][1000 genomes]
rs11618672	0.80[EUR][1000 genomes]
rs17071169	1.00[ASN][1000 genomes]
rs2025703	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41284209	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41287449	0.80[EUR][1000 genomes]
rs45465203	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56097393	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7326861	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7335662	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7337521	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981492	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9562785	0.85[EUR][1000 genomes]
rs9562786	0.85[EUR][1000 genomes]
rs9562790	0.85[EUR][1000 genomes]
rs9562791	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9562794	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9562795	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9562797	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562798	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562803	0.80[EUR][1000 genomes]
rs9567957	0.85[EUR][1000 genomes]
rs9567966	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567967	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567970	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567971	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567975	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567977	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567978	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567981	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567982	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567990	1.00[ASN][1000 genomes]
rs9567992	0.80[EUR][1000 genomes]
rs9568007	0.80[EUR][1000 genomes]
rs9634678	0.81[EUR][1000 genomes];0.90[ASN][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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9567983	MC5R	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48610400-48613200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:48610800-48613200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr13:48611000-48613400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr13:48611200-48613400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:48611800-48613600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr13:48612200-48613200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr13:48612200-48613200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr13:48612400-48613200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr13:48612400-48613200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr13:48612400-48613200	Flanking Active TSS	HepG2	liver
11	chr13:48612400-48613400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr13:48612400-48613400	Flanking Active TSS	Dnd41	blood
13	chr13:48612400-48613600	Flanking Active TSS	NHEK	skin
14	chr13:48612400-48625000	Weak transcription	Spleen	Spleen
15	chr13:48612600-48613200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr13:48612600-48613200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr13:48612600-48613200	Flanking Active TSS	Osteobl	bone
18	chr13:48612600-48613400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr13:48612600-48613400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr13:48612600-48613400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr13:48612600-48613400	Flanking Active TSS	HMEC	breast
22	chr13:48612600-48613600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:48612600-48613600	Enhancers	Small Intestine	intestine
24	chr13:48612600-48614200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:48612600-48615400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr13:48612600-48616000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr13:48612600-48616000	Weak transcription	Left Ventricle	heart
28	chr13:48612600-48616000	Weak transcription	Lung	lung
29	chr13:48612600-48623000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:48612600-48624200	Weak transcription	Gastric	stomach
31	chr13:48612600-48624800	Weak transcription	Ovary	ovary
32	chr13:48612600-48631600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:48612600-48640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr13:48612600-48645000	Weak transcription	Stomach Mucosa	stomach
35	chr13:48612800-48613200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr13:48612800-48613200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr13:48612800-48613200	Enhancers	Primary B cells from peripheral blood	blood
38	chr13:48612800-48613200	Enhancers	Primary T cells from cord blood	blood
39	chr13:48612800-48613200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr13:48612800-48613200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr13:48612800-48613200	Enhancers	Brain Cingulate Gyrus	brain
42	chr13:48612800-48613200	Enhancers	Brain Hippocampus Middle	brain
43	chr13:48612800-48613200	Enhancers	Colon Smooth Muscle	Colon
44	chr13:48612800-48613200	Enhancers	Fetal Heart	heart
45	chr13:48612800-48613200	Enhancers	Thymus	Thymus
46	chr13:48612800-48613200	Flanking Active TSS	NHLF	lung
47	chr13:48612800-48613400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr13:48612800-48613400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr13:48612800-48613400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr13:48612800-48613400	Enhancers	Brain Anterior Caudate	brain

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