Variant report

Variant	rs9487048
Chromosome Location	chr6:109615603-109615604
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr6:109615010-109615734	HCT-116	colon:	n/a	chr6:109615307-109615321
2	RFX5	chr6:109615308-109615641	Hela-S3	cervix:	n/a	n/a
3	TFAP2A	chr6:109615177-109615695	Hela-S3	cervix:	n/a	chr6:109615408-109615423 chr6:109615409-109615420 chr6:109615409-109615420 chr6:109615409-109615420 chr6:109615409-109615420
4	SMC3	chr6:109615264-109615613	Hela-S3	cervix:	n/a	n/a
5	SP1	chr6:109614956-109615753	HCT-116	colon:	n/a	chr6:109615307-109615321
6	MAX	chr6:109615212-109615632	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:109615126-109615622	HCT-116	colon:	n/a	n/a
8	MXI1	chr6:109615323-109615611	Hela-S3	cervix:	n/a	n/a
9	BRCA1	chr6:109615319-109615608	Hela-S3	cervix:	n/a	n/a
10	TFAP2C	chr6:109615107-109615732	Hela-S3	cervix:	n/a	chr6:109615408-109615423

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:109615579-109615629	H1-hESC	embryonic stem cell:	embryo
2	chr6:109615579-109615629	GM12891	blood:	n/a
3	chr6:109615579-109615629	AG04449	skin:	fetal
4	chr6:109615579-109615629	HCPEpiC	choroid plexus:	n/a
5	chr6:109615579-109615629	HL-60	blood:	n/a
6	chr6:109615579-109615629	HEK293	kidney:	embryo
7	chr6:109615579-109615629	GM06990	blood:	n/a
8	chr6:109615579-109615629	PrEC	prostate:	n/a
9	chr6:109615579-109615629	NT2-D1	testis:	n/a
10	chr6:109615579-109615629	SAEC	small airway:	n/a
11	chr6:109615579-109615629	AG09309	skin:	n/a
12	chr6:109615579-109615629	NHBE	bronchial:	n/a
13	chr6:109615579-109615629	HRCEpiC	kidney:	n/a
14	chr6:109615579-109615629	IMR90	lung:	fetal
15	chr6:109615579-109615629	HCT-116	colon:	n/a
16	chr6:109615579-109615629	HIPEpiC	eye:	n/a
17	chr6:109615579-109615629	RPTEC	kidney:	n/a
18	chr6:109615579-109615629	MCF-7	breast:	n/a
19	chr6:109615579-109615629	AG10803	skin:	n/a
20	chr6:109615579-109615629	SKMC	muscle:	n/a
21	chr6:109615579-109615629	ovcar-3	ovarian:	n/a
22	chr6:109615579-109615629	PANC-1	pancreas:	n/a
23	chr6:109615579-109615629	MCF10A-Er-Src	breast:	n/a
24	chr6:109615579-109615629	AoSMC	blood vessel:	n/a
25	chr6:109615579-109615629	ProgFib	skin:	n/a
26	chr6:109615579-109615629	HRPEpiC	eye:	n/a
27	chr6:109615579-109615629	ECC-1	luminal epithelium:	n/a
28	chr6:109615579-109615629	HepG2	liver:	n/a
29	chr6:109615579-109615629	HPAEpiC	pulmonary alveolar:	n/a
30	chr6:109615579-109615629	Jurkat	blood:	n/a
31	chr6:109615579-109615629	A549	lung:	n/a
32	chr6:109615579-109615629	NB4	blood:	n/a
33	chr6:109615579-109615629	PFSK-1	brain:	n/a
34	chr6:109615579-109615629	HCM	heart:	n/a
35	chr6:109615579-109615629	U87	brain:	n/a
36	chr6:109615579-109615629	Hepatocyte	liver:	n/a
37	chr6:109615579-109615629	LNCaP	prostate:	n/a
38	chr6:109615579-109615629	HAEpiC	amniotic membrane:	n/a
39	chr6:109615579-109615629	HNPCEpiC	eye:	n/a
40	chr6:109615579-109615629	CMK	blood:	n/a
41	chr6:109615579-109615629	AG09319	gingival:	n/a
42	chr6:109615579-109615629	AG04450	lung:	fetal
43	chr6:109615579-109615629	SK-N-MC	brain:	n/a
44	chr6:109615579-109615629	SK-N-SH	brain:	n/a
45	chr6:109615579-109615629	HEEpiC	esophagus:	n/a
46	chr6:109615579-109615629	SK-N-SH_RA	brain:	n/a
47	chr6:109615579-109615629	GM12878	blood:	n/a
48	chr6:109615579-109615629	HMEC	breast:	n/a
49	chr6:109615579-109615629	GM12892	blood:	n/a
50	chr6:109615579-109615629	HRE	kidney:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109414698..109417421-chr6:109614595..109617032,3	MCF-7	breast:
2	chr6:109613644..109615634-chr6:109701677..109704002,2	K562	blood:
3	chr6:109613797..109616312-chr6:109702118..109704634,2	MCF-7	breast:

No data

Variant related genes	Relation type
PTCHD3P3	TF binding region
ENSG00000238474	TF binding region
PTCHD3P3	CpG island
ENSG00000238474	CpG island
ENSG00000183137	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1008084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1111863	0.88[CEU][hapmap]
rs1111865	0.88[CEU][hapmap]
rs1111866	0.88[CEU][hapmap]
rs11153165	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs11153166	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs11153167	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11153168	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11751953	0.94[ASN][1000 genomes]
rs11757567	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961369	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966072	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12664455	0.90[ASN][1000 genomes]
rs13191948	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196219	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13196590	0.83[CEU][hapmap]
rs13200047	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13203155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13219432	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219561	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521908	0.85[CEU][hapmap]
rs1546723	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351724	0.84[CEU][hapmap]
rs351725	0.84[CEU][hapmap]
rs351728	0.83[CEU][hapmap]
rs4548045	0.85[ASN][1000 genomes]
rs4601178	0.88[CEU][hapmap]
rs5005289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55677234	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs59272337	0.92[ASN][1000 genomes]
rs6568569	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568570	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568571	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919423	0.83[CEU][hapmap]
rs6924815	0.85[CEU][hapmap]
rs7748918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772602	0.88[CEU][hapmap]
rs7773490	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs932223	0.83[CEU][hapmap]
rs9374076	0.94[ASN][1000 genomes]
rs9374080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374081	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9386779	0.85[ASN][1000 genomes]
rs9386790	0.88[CEU][hapmap]
rs9386791	0.83[CEU][hapmap]
rs9386795	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400265	0.94[ASN][1000 genomes]
rs9400269	0.88[CEU][hapmap]
rs9400271	0.85[CEU][hapmap]
rs9400272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480921	0.88[CEU][hapmap]
rs9480922	0.85[CEU][hapmap]
rs9480923	0.88[CEU][hapmap]
rs9480924	0.82[CHB][hapmap];0.82[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487023	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9487033	0.88[CEU][hapmap]
rs9487034	0.88[CEU][hapmap]
rs9487036	0.83[CEU][hapmap]
rs9487049	0.94[ASN][1000 genomes]
rs9487051	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487052	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109611200-109618200	Weak transcription	Gastric	stomach
2	chr6:109613000-109619000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:109613200-109619000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:109613400-109620200	Weak transcription	Right Atrium	heart
5	chr6:109613600-109615800	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr6:109613600-109617800	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:109613600-109620600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr6:109613800-109617400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:109613800-109618200	Weak transcription	Brain Anterior Caudate	brain
10	chr6:109614000-109618200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:109614000-109618400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:109614000-109618600	Weak transcription	Brain Angular Gyrus	brain
13	chr6:109614000-109619000	Weak transcription	Brain Substantia Nigra	brain
14	chr6:109614000-109622000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:109614200-109618400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:109614200-109619000	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:109614400-109621000	Enhancers	Primary hematopoietic stem cells	blood
18	chr6:109614600-109615800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:109614600-109616000	Enhancers	Fetal Heart	heart
20	chr6:109614600-109619400	Enhancers	HepG2	liver
21	chr6:109614800-109624400	Enhancers	K562	blood
22	chr6:109615000-109616000	Enhancers	Colon Smooth Muscle	Colon
23	chr6:109615000-109619600	Enhancers	Fetal Intestine Large	intestine
24	chr6:109615200-109615800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:109615200-109615800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:109615200-109615800	Enhancers	Duodenum Mucosa	Duodenum
27	chr6:109615200-109615800	Enhancers	Psoas Muscle	Psoas
28	chr6:109615200-109617000	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr6:109615200-109619400	Enhancers	Stomach Mucosa	stomach
30	chr6:109615200-109619800	Enhancers	Fetal Intestine Small	intestine
31	chr6:109615400-109615800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr6:109615400-109615800	Enhancers	Stomach Smooth Muscle	stomach
33	chr6:109615400-109617400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:109615400-109618400	Weak transcription	Small Intestine	intestine
35	chr6:109615400-109624600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:109615600-109615800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr6:109615600-109616200	Enhancers	Hela-S3	cervix
38	chr6:109615600-109616800	Weak transcription	Primary B cells from cord blood	blood
39	chr6:109615600-109617000	Weak transcription	Pancreas	Pancrea
40	chr6:109615600-109617600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr6:109615600-109617800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:109615600-109617800	Weak transcription	NHDF-Ad	bronchial
43	chr6:109615600-109618000	Weak transcription	Placenta	Placenta
44	chr6:109615600-109618200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:109615600-109618200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:109615600-109618200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:109615600-109618400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:109615600-109618400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:109615600-109619000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:109615600-109619200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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