Variant report

Variant	rs10512256
Chromosome Location	chr9:100686815-100686816
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:100686639-100687140	Raji	blood:	n/a	n/a
2	SPI1	chr9:100686690-100686963	K562	blood:	n/a	chr9:100686850-100686863 chr9:100686935-100686942
3	EP300	chr9:100686677-100687139	K562	blood:	n/a	n/a
4	POLR2A	chr9:100686775-100687020	K562	blood:	n/a	n/a
5	SPI1	chr9:100686737-100686967	K562	blood:	n/a	chr9:100686850-100686863 chr9:100686935-100686942
6	CCNT2	chr9:100686758-100686947	K562	blood:	n/a	n/a
7	POLR2A	chr9:100686807-100687362	K562	blood:	n/a	n/a
8	SPI1	chr9:100686648-100687164	HL-60	blood:	n/a	chr9:100686850-100686863 chr9:100686935-100686942
9	RCOR1	chr9:100686720-100687217	K562	blood:	n/a	n/a
10	TEAD4	chr9:100686653-100687166	K562	blood:	n/a	chr9:100687124-100687133
11	POLR2A	chr9:100686213-100687319	PBDE	blood:	n/a	n/a
12	GTF2B	chr9:100686699-100686906	K562	blood:	n/a	n/a
13	SPI1	chr9:100686586-100687335	HL-60	blood:	n/a	chr9:100686850-100686863 chr9:100686935-100686942
14	TBL1XR1	chr9:100685310-100686884	K562	blood:	n/a	n/a
15	CEBPB	chr9:100686690-100687074	K562	blood:	n/a	chr9:100686753-100686766 chr9:100686755-100686766
16	SPI1	chr9:100686632-100687037	GM12891	blood:	n/a	chr9:100686850-100686863 chr9:100686935-100686942
17	SPI1	chr9:100686656-100686967	GM12891	blood:	n/a	chr9:100686850-100686863 chr9:100686935-100686942
18	SPI1	chr9:100686711-100687053	GM12878	blood:	n/a	chr9:100686850-100686863 chr9:100686935-100686942

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100682029..100688801-chr9:100740969..100749393,29	MCF-7	breast:
2	chr9:100685020..100686845-chr9:100716549..100717520,12	K562	blood:
3	chr9:100682922..100687440-chr9:100817123..100820939,8	MCF-7	breast:
4	chr9:100685586..100688165-chr9:100878796..100881297,2	K562	blood:
5	chr9:100685412..100687157-chr9:100698092..100700080,2	MCF-7	breast:
6	chr9:100685930..100687826-chr9:100769901..100771666,3	K562	blood:
7	chr9:100685576..100688537-chr9:100780625..100782385,2	K562	blood:
8	chr9:100684661..100686943-chr9:100794140..100799259,5	K562	blood:
9	chr9:100393929..100396893-chr9:100683273..100687162,3	K562	blood:
10	chr9:100684640..100686948-chr9:100880759..100882563,2	K562	blood:
11	chr9:100683337..100688322-chr9:101015638..101019207,5	MCF-7	breast:
12	chr9:100678422..100708679-chr9:100734559..100755577,174	K562	blood:
13	chr9:100683079..100687048-chr9:101015405..101020638,4	K562	blood:
14	chr9:100685514..100687681-chr9:100731460..100733588,2	K562	blood:
15	chr9:100686261..100688755-chr9:100806613..100809213,2	K562	blood:
16	chr9:100682507..100691249-chr9:100739828..100748095,35	MCF-7	breast:
17	chr9:100685001..100687073-chr9:100804782..100806329,2	K562	blood:
18	chr2:131894199..131896837-chr9:100685147..100687682,2	MCF-7	breast:
19	chr9:100685127..100688021-chr9:100778345..100779899,2	MCF-7	breast:
20	chr9:100686277..100688519-chr9:100689376..100691185,2	MCF-7	breast:
21	chr9:100675954..100709047-chr9:100737887..100755543,175	K562	blood:
22	chr9:100686308..100689678-chr9:101021142..101024168,3	MCF-7	breast:
23	chr9:100683227..100687367-chr9:100758311..100762778,5	K562	blood:

No data

Variant related genes	Relation type
C9orf156	TF binding region
ENSG00000095383	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000136937	Chromatin interaction
ENSG00000236896	Chromatin interaction
ENSG00000212521	Chromatin interaction
ENSG00000136925	Chromatin interaction
ENSG00000106785	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10115216	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10512255	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1059003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs10739526	1.00[YRI][hapmap]
rs10760011	1.00[YRI][hapmap]
rs10983892	0.82[EUR][1000 genomes]
rs10983893	0.82[EUR][1000 genomes]
rs10983896	0.82[EUR][1000 genomes]
rs10984009	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs10984098	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10984253	1.00[YRI][hapmap]
rs10984377	1.00[CEU][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]
rs10984516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984522	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984545	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004762	1.00[YRI][hapmap]
rs12006522	1.00[YRI][hapmap]
rs12156487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375612	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12376113	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13295123	0.82[EUR][1000 genomes]
rs1348387	1.00[CEU][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]
rs1443433	0.82[GIH][hapmap]
rs1561957	1.00[YRI][hapmap]
rs17687621	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs1947015	0.91[CEU][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]
rs2120262	1.00[YRI][hapmap]
rs3808893	1.00[YRI][hapmap]
rs3824495	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4514106	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742708	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4743144	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4743149	0.93[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55978521	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027221	1.00[YRI][hapmap]
rs7031386	1.00[YRI][hapmap]
rs7032302	0.82[EUR][1000 genomes]
rs7034336	1.00[YRI][hapmap]
rs7036589	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7037172	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038998	1.00[YRI][hapmap]
rs7043516	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs7048255	1.00[YRI][hapmap]
rs72753506	0.82[EUR][1000 genomes]
rs72753508	0.82[EUR][1000 genomes]
rs72753537	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72753557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753579	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753581	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753588	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851498	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854948	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299258	0.90[LWK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10512256	C9orf156	cis	cerebellum	SCAN
rs10512256	ZNF782	cis	parietal	SCAN
rs10512256	GALNT12	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100684000-100687200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr9:100685000-100687000	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr9:100685000-100687200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:100685000-100687200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr9:100685200-100687600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:100685400-100687800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr9:100685600-100687200	Enhancers	Primary B cells from peripheral blood	blood
8	chr9:100686000-100687000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr9:100686000-100687400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr9:100686200-100687200	Enhancers	Primary T cells from cord blood	blood
11	chr9:100686200-100690800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr9:100686200-100691400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:100686200-100692200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr9:100686200-100692200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr9:100686400-100687200	Enhancers	GM12878-XiMat	blood
16	chr9:100686400-100690800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:100686600-100687000	Bivalent Enhancer	A549	lung
18	chr9:100686600-100687000	Enhancers	Dnd41	blood
19	chr9:100686600-100687200	Enhancers	K562	blood
20	chr9:100686600-100690600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr9:100686600-100690600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:100686600-100690600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr9:100686600-100691000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:100686800-100687000	Enhancers	Primary B cells from cord blood	blood
25	chr9:100686800-100687000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
26	chr9:100686800-100687000	Enhancers	Brain Substantia Nigra	brain
27	chr9:100686800-100687000	Bivalent Enhancer	HepG2	liver
28	chr9:100686800-100687200	Enhancers	Fetal Thymus	thymus
29	chr9:100686800-100690600	Weak transcription	Thymus	Thymus
30	chr9:100686800-100691200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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