Variant report

Variant	rs1541144
Chromosome Location	chr9:26956768-26956769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:135)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:135 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr9:26955747-26957272	IMR90	lung:	n/a	n/a
2	CCNT2	chr9:26956299-26956888	K562	blood:	n/a	chr9:26956718-26956727
3	POLR2A	chr9:26955182-26957152	NB4	blood:	n/a	n/a
4	BRCA1	chr9:26955953-26956833	H1-hESC	embryonic stem cell:	n/a	chr9:26956299-26956308
5	SIN3AK20	chr9:26955796-26956863	MCF-7	breast:	n/a	n/a
6	MAX	chr9:26955000-26957093	NB4	blood:	n/a	n/a
7	POLR2A	chr9:26955884-26956789	U87	brain:	n/a	n/a
8	SIN3A	chr9:26955942-26956919	H1-hESC	embryonic stem cell:	n/a	n/a
9	MXI1	chr9:26955031-26957368	SK-N-SH	brain:	n/a	n/a
10	MAX	chr9:26955893-26956877	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr9:26955798-26956852	GM19193	blood:	n/a	n/a
12	CEBPB	chr9:26955881-26956851	H1-hESC	embryonic stem cell:	n/a	chr9:26956055-26956064 chr9:26956053-26956066 chr9:26956055-26956064 chr9:26956053-26956064 chr9:26956053-26956066 chr9:26956055-26956066 chr9:26956055-26956064 chr9:26956055-26956064
13	POLR2A	chr9:26955986-26956769	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr9:26955815-26956820	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr9:26955863-26956820	GM12891	blood:	n/a	n/a
16	POLR2A	chr9:26955604-26956995	HepG2	liver:	n/a	n/a
17	POLR2A	chr9:26955802-26956818	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr9:26956040-26956776	PFSK-1	brain:	n/a	n/a
19	GTF2F1	chr9:26956005-26956806	K562	blood:	n/a	n/a
20	POLR2A	chr9:26955976-26956835	H1-hESC	embryonic stem cell:	n/a	n/a
21	IRF1	chr9:26955380-26957063	K562	blood:	n/a	n/a
22	MXI1	chr9:26955572-26957094	GM12878	blood:	n/a	n/a
23	POLR2A	chr9:26955843-26956842	GM12892	blood:	n/a	n/a
24	POLR2A	chr9:26955146-26956874	GM12892	blood:	n/a	n/a
25	POLR2A	chr9:26956035-26956816	HCT-116	colon:	n/a	n/a
26	POLR2A	chr9:26953902-26957243	PBDE	blood:	n/a	n/a
27	MAFF	chr9:26956126-26957217	HepG2	liver:	n/a	n/a
28	POLR2A	chr9:26956060-26957112	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr9:26955802-26956974	IMR90	lung:	n/a	n/a
30	ZBTB33	chr9:26955707-26956851	SK-N-SH	brain:	n/a	chr9:26956299-26956308 chr9:26956300-26956310
31	CHD1	chr9:26956498-26957036	H1-hESC	embryonic stem cell:	n/a	n/a
32	MTA3	chr9:26955738-26957006	GM12878	blood:	n/a	n/a
33	ZBTB7A	chr9:26956607-26956773	HepG2	liver:	n/a	n/a
34	POLR2A	chr9:26955984-26956958	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr9:26956192-26956827	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr9:26956063-26956825	K562	blood:	n/a	n/a
37	ELF1	chr9:26956206-26956825	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:26955135-26957202	GM12878	blood:	n/a	n/a
39	MAX	chr9:26955862-26956908	HepG2	liver:	n/a	n/a
40	POLR2A	chr9:26956063-26956864	GM18951	blood:	n/a	n/a
41	ZBTB7A	chr9:26956622-26956799	K562	blood:	n/a	n/a
42	EP300	chr9:26955247-26957256	K562	blood:	n/a	chr9:26956501-26956510
43	POLR2A	chr9:26955999-26956774	MCF-7	breast:	n/a	n/a
44	MAZ	chr9:26955945-26956785	Hela-S3	cervix:	n/a	n/a
45	TEAD4	chr9:26956477-26956839	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr9:26955891-26957177	K562	blood:	n/a	n/a
47	UBTF	chr9:26955137-26956970	K562	blood:	n/a	n/a
48	MAX	chr9:26956081-26956869	K562	blood:	n/a	n/a
49	POLR2A	chr9:26955831-26956857	GM12892	blood:	n/a	n/a
50	TCF12	chr9:26955863-26956836	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:26890425..26894629-chr9:26953159..26958312,6	K562	blood:
2	chr4:39698961..39699836-chr9:26956008..26956989,2	NB4	blood:
3	chr9:26885787..26888366-chr9:26956613..26958846,2	MCF-7	breast:
4	chr9:26956517..26958466-chr9:26969685..26972625,2	MCF-7	breast:
5	chr3:73160107..73160624-chr9:26956008..26956843,2	NB4	blood:
6	chr9:26889862..26894629-chr9:26953159..26958871,9	K562	blood:
7	chr9:26891902..26893962-chr9:26955453..26958235,3	MCF-7	breast:
8	chr9:26943098..26949574-chr9:26949927..26957421,13	K562	blood:
9	chr19:49121917..49122814-chr9:26955996..26956794,2	NB4	blood:

No data

Variant related genes	Relation type
ENSG00000234676	TF binding region
ENSG00000223247	Chromatin interaction
ENSG00000063176	Chromatin interaction
ENSG00000096872	Chromatin interaction
ENSG00000063177	Chromatin interaction
ENSG00000137055	Chromatin interaction
ENSG00000078140	Chromatin interaction
ENSG00000120159	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10738762	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10757634	0.85[ASN][1000 genomes]
rs10757635	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10757636	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10812488	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10812502	0.84[ASN][1000 genomes]
rs10812503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10812504	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10812506	0.81[ASN][1000 genomes]
rs10812507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10812508	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10812509	0.80[JPT][hapmap]
rs10812510	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10812515	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10812517	0.81[JPT][hapmap]
rs10812518	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10967586	0.85[JPT][hapmap]
rs10967621	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967622	0.83[ASN][1000 genomes]
rs10967623	0.83[ASN][1000 genomes]
rs10967627	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967629	0.96[ASN][1000 genomes]
rs10967630	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967632	0.96[ASN][1000 genomes]
rs10967633	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967635	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs10967636	0.81[ASN][1000 genomes]
rs10967645	0.94[CHB][hapmap]
rs10967648	0.84[ASN][1000 genomes]
rs10967649	0.84[JPT][hapmap]
rs10967650	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10967652	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10967670	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10967678	0.81[JPT][hapmap]
rs10967679	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11534184	0.83[ASN][1000 genomes]
rs11555693	0.81[ASN][1000 genomes]
rs11562224	0.81[ASN][1000 genomes]
rs12235490	0.81[ASN][1000 genomes]
rs12237867	0.84[ASN][1000 genomes]
rs12337896	0.89[CHB][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17833941	0.81[JPT][hapmap]
rs1819539	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2184438	0.94[ASN][1000 genomes]
rs2184439	0.92[ASN][1000 genomes]
rs2225720	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3739544	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs3758218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413873	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4621911	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs55827505	0.83[ASN][1000 genomes]
rs55870543	0.80[ASN][1000 genomes]
rs57450012	0.83[ASN][1000 genomes]
rs59159685	0.82[ASN][1000 genomes]
rs60841248	0.81[ASN][1000 genomes]
rs6475945	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs6475947	0.86[CEU][hapmap];0.84[YRI][hapmap]
rs6475954	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7018585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7020010	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs7034115	0.96[ASN][1000 genomes]
rs7034478	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034670	0.81[AMR][1000 genomes]
rs7034888	0.81[ASN][1000 genomes]
rs7034899	0.81[ASN][1000 genomes]
rs7035447	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs7038218	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7040505	0.83[CHB][hapmap];0.85[JPT][hapmap];0.97[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7042133	0.83[ASN][1000 genomes]
rs7042447	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7849248	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7854191	0.83[EUR][1000 genomes]
rs7856462	0.86[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs7857447	0.81[JPT][hapmap]
rs7857669	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7860542	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7863476	0.90[CEU][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7865952	0.82[ASN][1000 genomes]
rs7868158	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs7870787	0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7871668	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7872496	0.85[JPT][hapmap]
rs7874940	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7875068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875171	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]

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	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
3	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1541144	IFT74	Cis_1M	lymphoblastoid	RTeQTL
rs1541144	ENSG00000096872	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26954800-26958200	Active TSS	K562	blood
2	chr9:26955200-26956800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr9:26955200-26957000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:26955200-26957000	Active TSS	Colonic Mucosa	Colon
5	chr9:26955200-26957000	Active TSS	Gastric	stomach
6	chr9:26955200-26957200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:26955200-26957200	Active TSS	Rectal Smooth Muscle	rectum
8	chr9:26955200-26957400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:26955200-26957400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:26955200-26957600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:26955200-26957800	Active TSS	Fetal Brain Male	brain
12	chr9:26955200-26957800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr9:26955400-26956800	Active TSS	Small Intestine	intestine
14	chr9:26955400-26956800	Bivalent/Poised TSS	HepG2	liver
15	chr9:26955400-26957000	Active TSS	Fetal Lung	lung
16	chr9:26955400-26957200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr9:26955400-26957200	Active TSS	Fetal Stomach	stomach
18	chr9:26955400-26957200	Active TSS	Right Atrium	heart
19	chr9:26955400-26957200	Active TSS	Right Ventricle	heart
20	chr9:26955400-26957400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:26955400-26957400	Active TSS	Stomach Smooth Muscle	stomach
22	chr9:26955400-26957400	Active TSS	A549	lung
23	chr9:26955600-26956800	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr9:26955600-26956800	Active TSS	Liver	Liver
25	chr9:26955600-26956800	Active TSS	Brain Anterior Caudate	brain
26	chr9:26955600-26956800	Active TSS	Brain Hippocampus Middle	brain
27	chr9:26955600-26956800	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr9:26955600-26956800	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr9:26955600-26957000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:26955600-26957000	Active TSS	Brain Cingulate Gyrus	brain
31	chr9:26955600-26957000	Active TSS	Fetal Brain Female	brain
32	chr9:26955600-26957000	Active TSS	Fetal Intestine Large	intestine
33	chr9:26955600-26957000	Active TSS	Fetal Muscle Leg	muscle
34	chr9:26955600-26957000	Active TSS	Placenta	Placenta
35	chr9:26955600-26957000	Active TSS	Pancreas	Pancrea
36	chr9:26955600-26957200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:26955600-26957200	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr9:26955600-26957200	Active TSS	Brain Angular Gyrus	brain
39	chr9:26955600-26957200	Active TSS	Brain Germinal Matrix	brain
40	chr9:26955600-26957200	Active TSS	Psoas Muscle	Psoas
41	chr9:26955600-26957200	Active TSS	HSMMtube	muscle
42	chr9:26955600-26957400	Active TSS	H1 Cell Line	embryonic stem cell
43	chr9:26955600-26957400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:26955600-26957400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:26955600-26957400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:26955600-26957400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:26955600-26957400	Active TSS	NH-A	brain
48	chr9:26955600-26957600	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr9:26955600-26957600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:26955600-26957600	Active TSS	NHDF-Ad	bronchial

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