Variant report

Variant	rs10812500
Chromosome Location	chr9:26946576-26946577
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr9:26945575-26948341	NB4	blood:	n/a	n/a
2	MAX	chr9:26946251-26947774	Hela-S3	cervix:	n/a	n/a
3	REST	chr9:26945977-26948038	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr9:26945741-26948332	H1-hESC	embryonic stem cell:	n/a	n/a
5	GATA1	chr9:26945386-26948919	PBDE	blood:	n/a	chr9:26948836-26948857 chr9:26948839-26948850
6	WRNIP1	chr9:26946164-26946969	GM12878	blood:	n/a	n/a
7	TAF1	chr9:26946474-26947830	H1-hESC	embryonic stem cell:	n/a	n/a
8	GABPA	chr9:26946441-26948107	MCF-7	breast:	n/a	chr9:26947474-26947483
9	MXI1	chr9:26946549-26947770	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr9:26946555-26947750	K562	blood:	n/a	n/a
11	POLR2A	chr9:26945574-26948342	GM12891	blood:	n/a	n/a
12	CHD1	chr9:26945731-26948413	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr9:26946493-26947815	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr9:26945760-26948285	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr9:26946558-26948456	NB4	blood:	n/a	n/a
16	RUNX3	chr9:26946486-26947752	GM12878	blood:	n/a	n/a
17	MXI1	chr9:26946574-26948062	GM12878	blood:	n/a	n/a
18	SIN3A	chr9:26946301-26948088	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF384	chr9:26946544-26946700	GM12878	blood:	n/a	n/a
20	POLR2A	chr9:26946335-26948319	GM12878	blood:	n/a	n/a
21	POLR2A	chr9:26946366-26948187	MCF10A-Er-Src	breast:	n/a	n/a
22	STAT5A	chr9:26946533-26947830	GM12878	blood:	n/a	chr9:26947491-26947499
23	MAZ	chr9:26946018-26948128	IMR90	lung:	n/a	n/a
24	MYC	chr9:26945612-26948147	NB4	blood:	n/a	n/a
25	POLR2A	chr9:26946545-26948037	Hela-S3	cervix:	n/a	n/a
26	MXI1	chr9:26945295-26948354	SK-N-SH	brain:	n/a	n/a
27	HCFC1	chr9:26946553-26948105	Hela-S3	cervix:	n/a	n/a
28	MTA3	chr9:26946495-26947820	GM12878	blood:	n/a	n/a
29	POLR2A	chr9:26946395-26948256	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:26946561-26946611	CMK	blood:	n/a
2	chr9:26946561-26946611	SK-N-SH	brain:	n/a
3	chr9:26946561-26946611	HPAEpiC	pulmonary alveolar:	n/a
4	chr9:26946561-26946611	NT2-D1	testis:	n/a
5	chr9:26946561-26946611	HRPEpiC	eye:	n/a
6	chr9:26946561-26946611	HCM	heart:	n/a
7	chr9:26946561-26946611	Caco-2	colon:	n/a
8	chr9:26946561-26946611	GM19239	blood:	n/a
9	chr9:26946561-26946611	A549	lung:	n/a
10	chr9:26946561-26946611	NB4	blood:	n/a
11	chr9:26946561-26946611	SKMC	muscle:	n/a
12	chr9:26946561-26946611	ProgFib	skin:	n/a
13	chr9:26946561-26946611	IMR90	lung:	fetal
14	chr9:26946561-26946611	Hepatocyte	liver:	n/a
15	chr9:26946561-26946611	HCT-116	colon:	n/a
16	chr9:26946561-26946611	SK-N-MC	brain:	n/a
17	chr9:26946561-26946611	HNPCEpiC	eye:	n/a
18	chr9:26946561-26946611	AG04450	lung:	fetal
19	chr9:26946561-26946611	BE2_C	brain:	n/a
20	chr9:26946561-26946611	GM06990	blood:	n/a
21	chr9:26946561-26946611	NHBE	bronchial:	n/a
22	chr9:26946561-26946611	HRCEpiC	kidney:	n/a
23	chr9:26946561-26946611	AG04449	skin:	fetal
24	chr9:26946561-26946611	MCF-7	breast:	n/a
25	chr9:26946561-26946611	H1-hESC	embryonic stem cell:	embryo
26	chr9:26946561-26946611	Hela-S3	cervix:	n/a
27	chr9:26946561-26946611	HL-60	blood:	n/a
28	chr9:26946561-26946611	ECC-1	luminal epithelium:	n/a
29	chr9:26946561-26946611	HEEpiC	esophagus:	n/a
30	chr9:26946561-26946611	HCF	heart:	n/a
31	chr9:26946561-26946611	PANC-1	pancreas:	n/a
32	chr9:26946561-26946611	T-47D	breast:	n/a
33	chr9:26946561-26946611	GM12891	blood:	n/a
34	chr9:26946561-26946611	SK-N-SH_RA	brain:	n/a
35	chr9:26946561-26946611	U87	brain:	n/a
36	chr9:26946561-26946611	AoSMC	blood vessel:	n/a
37	chr9:26946561-26946611	PFSK-1	brain:	n/a
38	chr9:26946561-26946611	HepG2	liver:	n/a
39	chr9:26946561-26946611	K562	blood:	n/a
40	chr9:26946561-26946611	NH-A	brain:	n/a
41	chr9:26946561-26946611	HAEpiC	amniotic membrane:	n/a
42	chr9:26946561-26946611	ovcar-3	ovarian:	n/a
43	chr9:26946561-26946611	HCPEpiC	choroid plexus:	n/a
44	chr9:26946561-26946611	HRE	kidney:	n/a
45	chr9:26946561-26946611	SAEC	small airway:	n/a
46	chr9:26946561-26946611	HUVEC	blood vessel:	n/a
47	chr9:26946561-26946611	NHDF-neo	bronchial:	n/a
48	chr9:26946561-26946611	RPTEC	kidney:	n/a
49	chr9:26946561-26946611	GM12892	blood:	n/a
50	chr9:26946561-26946611	HEK293	kidney:	embryo

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:26891080..26894676-chr9:26945695..26949113,9	K562	blood:
2	chr9:26891080..26895841-chr9:26945501..26948974,8	K562	blood:
3	chr9:26890485..26893190-chr9:26945159..26948755,7	MCF-7	breast:
4	chr9:26943098..26949574-chr9:26949927..26957421,13	K562	blood:
5	chr9:26863474..26865685-chr9:26944202..26946970,2	K562	blood:
6	chr9:26890972..26893985-chr9:26945405..26948624,3	MCF-7	breast:
7	chr9:26945881..26949167-chr9:26974909..26976838,3	MCF-7	breast:
8	chr9:26920077..26923896-chr9:26945076..26948067,5	MCF-7	breast:
9	chr6:27114345..27115100-chr9:26946364..26947201,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
IFT74	TF binding region
IFT74	CpG island
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000096872	Chromatin interaction
ENSG00000137055	Chromatin interaction
ENSG00000240306	Chromatin interaction
ENSG00000234676	Chromatin interaction
ENSG00000120159	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10283643	1.00[CHB][hapmap]
rs10511793	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10812492	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967593	1.00[CHB][hapmap]
rs10967594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967624	1.00[CHB][hapmap]
rs10967625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10967634	1.00[CHB][hapmap]
rs10967639	1.00[CHB][hapmap]
rs10967640	1.00[CHB][hapmap]
rs1161603	1.00[CHB][hapmap]
rs11788136	1.00[CHB][hapmap]
rs12001845	1.00[CHB][hapmap]
rs12002260	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004732	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12005388	1.00[CHB][hapmap]
rs12337860	1.00[CHB][hapmap]
rs12338678	1.00[CHB][hapmap]
rs12339162	1.00[CHB][hapmap]
rs12340500	1.00[CHB][hapmap]
rs12342005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343345	1.00[CHB][hapmap]
rs12345094	1.00[CHB][hapmap]
rs12349359	1.00[CHB][hapmap]
rs12352441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12352603	1.00[CHB][hapmap]
rs12352631	1.00[CHB][hapmap]
rs12554485	1.00[CHB][hapmap]
rs13293051	1.00[CHB][hapmap]
rs16910888	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16910895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16911083	1.00[CHB][hapmap]
rs17694121	1.00[CHB][hapmap]
rs17694140	1.00[CHB][hapmap]
rs17694300	1.00[CHB][hapmap]
rs17694306	1.00[CHB][hapmap]
rs17694549	1.00[CHB][hapmap]
rs17694796	1.00[CHB][hapmap]
rs17755887	1.00[CHB][hapmap]
rs17755911	1.00[CHB][hapmap]
rs17756599	1.00[CHB][hapmap]
rs17756667	1.00[CHB][hapmap]
rs17756685	1.00[CHB][hapmap]
rs2027124	1.00[CHB][hapmap]
rs2152063	1.00[CHB][hapmap]
rs2991949	1.00[CHB][hapmap]
rs3429	1.00[CHB][hapmap]
rs596427	1.00[CHB][hapmap]
rs615532	1.00[CHB][hapmap]
rs62542667	0.86[ASN][1000 genomes]
rs62544439	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544444	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6475945	0.83[CEU][hapmap]
rs6475947	0.83[CEU][hapmap]
rs6475948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475959	1.00[CHB][hapmap]
rs6475963	1.00[CHB][hapmap]
rs6475966	1.00[CHB][hapmap]
rs6475968	1.00[CHB][hapmap]
rs7019692	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7037860	1.00[CHB][hapmap]
rs7038218	0.88[CEU][hapmap]
rs7039400	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7040516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040772	1.00[CHB][hapmap]
rs7042003	1.00[CHB][hapmap]
rs7042119	1.00[CHB][hapmap]
rs7042447	0.83[CEU][hapmap]
rs7044842	1.00[CHB][hapmap]
rs73436047	0.86[ASN][1000 genomes]
rs7847280	1.00[CHB][hapmap]
rs7851582	1.00[ASN][1000 genomes]
rs7856462	0.83[CEU][hapmap]
rs7860542	0.85[CEU][hapmap]
rs7868158	0.82[CEU][hapmap]
rs7871097	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871286	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873019	1.00[CHB][hapmap]
rs7873161	1.00[CHB][hapmap]
rs7873329	1.00[CHB][hapmap]

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	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10812500	IFT74	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26940000-26948400	Active TSS	GM12878-XiMat	blood
2	chr9:26944600-26948400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr9:26944800-26948000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr9:26945200-26947800	Active TSS	HMEC	breast
5	chr9:26945200-26948000	Active TSS	NHLF	lung
6	chr9:26945200-26948200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr9:26945200-26948200	Active TSS	K562	blood
8	chr9:26945200-26948400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr9:26945200-26948400	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr9:26945400-26946600	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr9:26945400-26946800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:26945400-26946800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr9:26945400-26948000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr9:26945400-26948200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr9:26945600-26946600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr9:26945600-26946600	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr9:26945600-26946600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr9:26945600-26946600	Enhancers	Spleen	Spleen
19	chr9:26945600-26946800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:26945600-26946800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:26945600-26946800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:26945600-26946800	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr9:26945600-26946800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr9:26945600-26947000	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr9:26945600-26947000	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr9:26945600-26947000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr9:26945600-26947000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr9:26945600-26947800	Active TSS	Esophagus	oesophagus
29	chr9:26945600-26948200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr9:26945600-26948200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:26945600-26948200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:26945600-26948200	Active TSS	Right Atrium	heart
33	chr9:26945600-26948400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr9:26945600-26948400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:26945800-26946600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr9:26945800-26946600	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr9:26945800-26947800	Active TSS	Muscle Satellite Cultured Cells	--
38	chr9:26945800-26948000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr9:26945800-26948000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:26945800-26948000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:26945800-26948000	Active TSS	Fetal Muscle Trunk	muscle
42	chr9:26945800-26948000	Active TSS	Left Ventricle	heart
43	chr9:26945800-26948000	Active TSS	Lung	lung
44	chr9:26945800-26948000	Active TSS	Ovary	ovary
45	chr9:26945800-26948000	Active TSS	Pancreas	Pancrea
46	chr9:26945800-26948000	Active TSS	Right Ventricle	heart
47	chr9:26945800-26948000	Active TSS	HSMM	muscle
48	chr9:26945800-26948200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:26945800-26948200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:26945800-26948200	Active TSS	Fetal Kidney	kidney

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