Variant report

Variant	rs9388486
Chromosome Location	chr6:126661154-126661155
allele	C/T
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	chr6:126660726-126661738	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr6:126660901-126661539	MCF10A-Er-Src	breast:	n/a	n/a
3	EGR1	chr6:126660930-126661479	MCF-7	breast:	n/a	chr6:126661213-126661223 chr6:126661209-126661223
4	ETS1	chr6:126661069-126661438	A549	lung:	n/a	chr6:126661211-126661222
5	E2F4	chr6:126660939-126661871	Hela-S3	cervix:	n/a	chr6:126661147-126661156 chr6:126661149-126661158 chr6:126661213-126661222
6	TBP	chr6:126661137-126661827	HepG2	liver:	n/a	n/a
7	MBD4	chr6:126660859-126661557	HepG2	liver:	n/a	n/a
8	SRF	chr6:126660903-126661576	MCF-7	breast:	n/a	chr6:126661248-126661258
9	MAX	chr6:126661081-126661614	HepG2	liver:	n/a	n/a
10	EGR1	chr6:126660952-126661392	H1-hESC	embryonic stem cell:	n/a	chr6:126661213-126661223 chr6:126661209-126661223
11	POLR2A	chr6:126660976-126661469	HepG2	liver:	n/a	n/a
12	TEAD4	chr6:126661069-126661536	H1-hESC	embryonic stem cell:	n/a	n/a
13	TEAD4	chr6:126660877-126661601	K562	blood:	n/a	n/a
14	JUND	chr6:126660920-126661546	H1-hESC	embryonic stem cell:	n/a	chr6:126661148-126661157
15	TBL1XR1	chr6:126661061-126661490	K562	blood:	n/a	n/a
16	EGR1	chr6:126660978-126661462	ECC-1	luminal epithelium:	n/a	chr6:126661213-126661223 chr6:126661209-126661223
17	MAZ	chr6:126660953-126661590	K562	blood:	n/a	n/a
18	MYC	chr6:126661028-126661820	NB4	blood:	n/a	chr6:126661790-126661799
19	POLR2A	chr6:126661124-126661529	GM12891	blood:	n/a	n/a
20	PAX5	chr6:126661026-126661431	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:126660890-126661873	HL-60	blood:	n/a	n/a
22	CEBPB	chr6:126660968-126661314	K562	blood:	n/a	n/a
23	YY1	chr6:126661091-126661549	ECC-1	luminal epithelium:	n/a	chr6:126661213-126661222
24	E2F4	chr6:126661058-126661512	GM12878	blood:	n/a	chr6:126661147-126661156 chr6:126661149-126661158 chr6:126661213-126661222
25	IRF4	chr6:126660900-126661449	GM12878	blood:	n/a	n/a
26	SMC3	chr6:126660980-126661750	Hela-S3	cervix:	n/a	n/a
27	TAF1	chr6:126661153-126661426	PFSK-1	brain:	n/a	n/a
28	SRF	chr6:126661115-126661371	HepG2	liver:	n/a	chr6:126661248-126661258
29	POLR2A	chr6:126661003-126661567	K562	blood:	n/a	n/a
30	SIN3AK20	chr6:126661100-126661461	H1-hESC	embryonic stem cell:	n/a	n/a
31	ELF1	chr6:126661053-126661545	GM12878	blood:	n/a	n/a
32	CBX3	chr6:126660794-126661584	K562	blood:	n/a	n/a
33	SIN3AK20	chr6:126661129-126661545	K562	blood:	n/a	n/a
34	SPI1	chr6:126661114-126661693	HL-60	blood:	n/a	n/a
35	SIN3AK20	chr6:126660871-126661732	HCT-116	colon:	n/a	n/a
36	TBP	chr6:126660973-126661601	K562	blood:	n/a	n/a
37	SP4	chr6:126660896-126661451	H1-hESC	embryonic stem cell:	n/a	chr6:126661210-126661226 chr6:126661212-126661223
38	TAF1	chr6:126660946-126661578	ECC-1	luminal epithelium:	n/a	n/a
39	MYBL2	chr6:126660903-126661737	HepG2	liver:	n/a	n/a
40	MYC	chr6:126661009-126661527	K562	blood:	n/a	n/a
41	GABPA	chr6:126661074-126661474	K562	blood:	n/a	chr6:126661213-126661222
42	POLR2A	chr6:126660869-126661641	H1-hESC	embryonic stem cell:	n/a	n/a
43	SIN3AK20	chr6:126661031-126661521	HepG2	liver:	n/a	n/a
44	TAF1	chr6:126661044-126661561	K562	blood:	n/a	n/a
45	POLR2A	chr6:126660909-126661494	MCF10A-Er-Src	breast:	n/a	n/a
46	CTCF	chr6:126661126-126661248	Lung_OC	lung:	n/a	n/a
47	ELF1	chr6:126660948-126661495	GM12878	blood:	n/a	n/a
48	SP1	chr6:126660976-126661447	GM12878	blood:	n/a	chr6:126661168-126661178 chr6:126661213-126661222 chr6:126661213-126661223 chr6:126661212-126661224 chr6:126661214-126661223 chr6:126661214-126661223 chr6:126661212-126661224 chr6:126661167-126661179 chr6:126661167-126661179 chr6:126661213-126661223 chr6:126661212-126661223
49	TAF1	chr6:126661039-126661540	K562	blood:	n/a	n/a
50	ELF1	chr6:126661050-126661420	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:126661136-126661186	U87	brain:	n/a
2	chr6:126661136-126661186	GM12878	blood:	n/a
3	chr6:126661136-126661186	Jurkat	blood:	n/a
4	chr6:126661136-126661186	AG04449	skin:	fetal
5	chr6:126661136-126661186	PANC-1	pancreas:	n/a
6	chr6:126661136-126661186	MCF10A-Er-Src	breast:	n/a
7	chr6:126661136-126661186	MCF-7	breast:	n/a
8	chr6:126661136-126661186	RPTEC	kidney:	n/a
9	chr6:126661136-126661186	HepG2	liver:	n/a
10	chr6:126661136-126661186	AG10803	skin:	n/a
11	chr6:126661136-126661186	GM12892	blood:	n/a
12	chr6:126661136-126661186	AG09319	gingival:	n/a
13	chr6:126661136-126661186	AG09309	skin:	n/a
14	chr6:126661136-126661186	HCPEpiC	choroid plexus:	n/a
15	chr6:126661136-126661186	Hepatocyte	liver:	n/a
16	chr6:126661136-126661186	LNCaP	prostate:	n/a
17	chr6:126661136-126661186	GM19239	blood:	n/a
18	chr6:126661136-126661186	HRCEpiC	kidney:	n/a
19	chr6:126661136-126661186	A549	lung:	n/a
20	chr6:126661136-126661186	NHBE	bronchial:	n/a
21	chr6:126661136-126661186	HL-60	blood:	n/a
22	chr6:126661136-126661186	GM12891	blood:	n/a
23	chr6:126661136-126661186	H1-hESC	embryonic stem cell:	embryo
24	chr6:126661136-126661186	PrEC	prostate:	n/a
25	chr6:126661136-126661186	PFSK-1	brain:	n/a
26	chr6:126661136-126661186	Caco-2	colon:	n/a
27	chr6:126661136-126661186	HEEpiC	esophagus:	n/a
28	chr6:126661136-126661186	ECC-1	luminal epithelium:	n/a
29	chr6:126661136-126661186	HUVEC	blood vessel:	n/a
30	chr6:126661136-126661186	SK-N-SH	brain:	n/a
31	chr6:126661136-126661186	IMR90	lung:	fetal
32	chr6:126661136-126661186	HCT-116	colon:	n/a
33	chr6:126661136-126661186	K562	blood:	n/a
34	chr6:126661136-126661186	AG04450	lung:	fetal
35	chr6:126661136-126661186	HEK293	kidney:	embryo
36	chr6:126661136-126661186	HCF	heart:	n/a
37	chr6:126661136-126661186	T-47D	breast:	n/a
38	chr6:126661136-126661186	AoSMC	blood vessel:	n/a
39	chr6:126661136-126661186	HNPCEpiC	eye:	n/a
40	chr6:126661136-126661186	GM06990	blood:	n/a
41	chr6:126661136-126661186	ProgFib	skin:	n/a
42	chr6:126661136-126661186	Hela-S3	cervix:	n/a
43	chr6:126661136-126661186	SKMC	muscle:	n/a
44	chr6:126661136-126661186	NHDF-neo	bronchial:	n/a
45	chr6:126661136-126661186	BE2_C	brain:	n/a
46	chr6:126661136-126661186	BJ	skin:	n/a
47	chr6:126661136-126661186	NB4	blood:	n/a
48	chr6:126661136-126661186	HCM	heart:	n/a
49	chr6:126661136-126661186	CMK	blood:	n/a
50	chr6:126661136-126661186	SK-N-SH_RA	brain:	n/a

Variant related genes	Relation type
CENPW	TF binding region
CENPW	CpG island

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10457478	1.00[ASN][1000 genomes]
rs1159619	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202204	1.00[ASN][1000 genomes]
rs1361108	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361262	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490384	1.00[ASN][1000 genomes]
rs1490387	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490388	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538172	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1578060	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591805	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1602278	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17754780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907067	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027299	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2039735	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2045258	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050644	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2130603	0.85[EUR][1000 genomes]
rs2326387	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34539692	1.00[ASN][1000 genomes]
rs4053271	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4422634	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895807	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895808	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59698523	0.85[EUR][1000 genomes]
rs6907898	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738135	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321065	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375435	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375442	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs9375446	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388487	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388489	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388490	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398803	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398804	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9401876	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9401885	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491624	1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3379370	chr6:126660674-126663387	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9388486	FABP7	cis	cerebellum	SCAN
rs9388486	C6orf174	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:126660600-126661400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:126660600-126661400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:126660600-126662400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:126660600-126663800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:126660800-126661200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:126660800-126661200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:126660800-126661200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:126660800-126661200	Flanking Active TSS	Dnd41	blood
9	chr6:126660800-126661200	Active TSS	HepG2	liver
10	chr6:126660800-126661200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr6:126660800-126661400	Active TSS	Brain Anterior Caudate	brain
12	chr6:126660800-126661600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:126660800-126661600	Active TSS	Primary B cells from cord blood	blood
14	chr6:126660800-126661600	Active TSS	Primary B cells from peripheral blood	blood
15	chr6:126660800-126661600	Active TSS	Primary hematopoietic stem cells	blood
16	chr6:126660800-126661600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:126660800-126661600	Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr6:126660800-126661600	Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr6:126660800-126661600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr6:126660800-126661600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr6:126660800-126661600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:126660800-126661600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:126660800-126661600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
24	chr6:126660800-126661600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr6:126660800-126661600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:126660800-126661600	Active TSS	Duodenum Mucosa	Duodenum
27	chr6:126660800-126661600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr6:126660800-126661600	Active TSS	Fetal Muscle Trunk	muscle
29	chr6:126660800-126661600	Active TSS	Placenta	Placenta
30	chr6:126660800-126661600	Active TSS	Rectal Smooth Muscle	rectum
31	chr6:126660800-126661600	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr6:126660800-126661800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr6:126660800-126661800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr6:126660800-126661800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:126660800-126661800	Active TSS	Brain Angular Gyrus	brain
36	chr6:126660800-126661800	Active TSS	Brain Cingulate Gyrus	brain
37	chr6:126660800-126661800	Active TSS	Brain Hippocampus Middle	brain
38	chr6:126660800-126661800	Active TSS	Colon Smooth Muscle	Colon
39	chr6:126660800-126661800	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr6:126660800-126661800	Active TSS	Fetal Brain Male	brain
41	chr6:126660800-126661800	Active TSS	Fetal Intestine Large	intestine
42	chr6:126660800-126661800	Active TSS	Fetal Intestine Small	intestine
43	chr6:126660800-126661800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr6:126660800-126661800	Active TSS	Fetal Lung	lung
45	chr6:126660800-126661800	Active TSS	Fetal Muscle Leg	muscle
46	chr6:126660800-126661800	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr6:126660800-126661800	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr6:126660800-126661800	Active TSS	Stomach Smooth Muscle	stomach
49	chr6:126660800-126661800	Active TSS	HUVEC	blood vessel
50	chr6:126660800-126661800	Active TSS	Osteobl	bone

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