Variant report

Variant	rs602347
Chromosome Location	chr11:64648049-64648050
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	ELK1	chr11:64647844-64648157	GM12878	blood:	n/a	n/a
2	RUNX3	chr11:64647704-64648492	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:64647688-64648131	GM12892	blood:	n/a	n/a
4	NFIC	chr11:64647861-64648634	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:64644871-64648628	Raji	blood:	n/a	n/a
6	RUNX3	chr11:64647785-64648608	GM12878	blood:	n/a	n/a
7	ATF2	chr11:64647920-64648533	GM12878	blood:	n/a	n/a
8	WRNIP1	chr11:64647987-64648287	GM12878	blood:	n/a	n/a
9	FOXM1	chr11:64647866-64648441	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:64645642-64648245	PANC-1	pancreas:	n/a	n/a
11	USF2	chr11:64647833-64648374	GM12878	blood:	n/a	n/a
12	EP300	chr11:64647895-64648535	GM12878	blood:	n/a	chr11:64648364-64648378 chr11:64648341-64648355
13	PML	chr11:64647503-64648631	GM12878	blood:	n/a	n/a
14	MXI1	chr11:64647850-64648489	GM12878	blood:	n/a	chr11:64648166-64648175
15	TBL1XR1	chr11:64647883-64648524	GM12878	blood:	n/a	n/a
16	EBF1	chr11:64647847-64648746	GM12878	blood:	n/a	chr11:64648627-64648637 chr11:64647992-64648003
17	BHLHE40	chr11:64647933-64648528	GM12878	blood:	n/a	n/a
18	RELA	chr11:64647785-64648538	GM19099	blood:	n/a	n/a
19	IKZF1	chr11:64647878-64648495	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:64645552-64648117	SK-N-MC	brain:	n/a	n/a
21	USF1	chr11:64648027-64648296	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:64647904-64648139	HCT-116	colon:	n/a	n/a
23	ATF3	chr11:64647996-64648357	GM12878	blood:	n/a	n/a
24	MAX	chr11:64647721-64648563	GM12878	blood:	n/a	chr11:64648164-64648175 chr11:64648163-64648172 chr11:64648165-64648174 chr11:64648156-64648172
25	MTA3	chr11:64647779-64648567	GM12878	blood:	n/a	n/a
26	JUN	chr11:64645356-64648134	K562	blood:	n/a	chr11:64647650-64647659

No.	Distal block	Cell Line	Cell type
1	chr11:64576838..64579724-chr11:64644602..64648695,4	K562	blood:
2	chr11:64645500..64648132-chr11:64701780..64703587,2	MCF-7	breast:
3	chr11:64543733..64546506-chr11:64646290..64648884,3	K562	blood:
4	chr11:64644806..64648507-chr11:64877927..64882201,4	MCF-7	breast:
5	chr11:64643878..64648186-chr11:64793107..64797470,5	K562	blood:
6	chr11:64543733..64546227-chr11:64645757..64648257,3	K562	blood:
7	chr11:64646527..64648346-chr11:64683617..64685265,2	MCF-7	breast:
8	chr11:64644503..64648099-chr11:64683052..64686363,9	K562	blood:
9	chr11:64647655..64649360-chr11:64811641..64813979,2	MCF-7	breast:
10	chr11:64646646..64648212-chr11:64949732..64952705,2	MCF-7	breast:
11	chr11:64642873..64648975-chr11:64779425..64783727,9	MCF-7	breast:
12	chr11:64646046..64648742-chr11:64862657..64865181,3	K562	blood:

Variant related genes	Relation type
EHD1	TF binding region
ENSG00000230835	TF binding region
ENSG00000254501	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000168060	Chromatin interaction
ENSG00000110046	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000133895	Chromatin interaction
ENSG00000270775	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000110025	Chromatin interaction
ENSG00000149735	Chromatin interaction
ENSG00000014216	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10897533	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1211284	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12573	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12801172	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17146413	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2007521	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2077026	0.98[ASN][1000 genomes]
rs3741391	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3893108	0.91[ASN][1000 genomes]
rs3936999	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs3937000	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs41381745	0.95[ASN][1000 genomes]
rs4930280	0.90[ASN][1000 genomes]
rs4930281	0.91[ASN][1000 genomes]
rs4930685	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57851864	0.97[ASN][1000 genomes]
rs589556	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs607569	0.91[ASN][1000 genomes]
rs620066	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs621608	0.98[ASN][1000 genomes]
rs622611	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs635722	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs641623	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs649208	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs653225	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs654580	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs656982	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7126744	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7926812	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7927560	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7943238	0.85[ASN][1000 genomes]
rs7944276	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7949887	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs7952306	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7952567	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
2	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
3	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
4	nsv897704	chr11:64584987-64701030	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
5	nsv897705	chr11:64591679-64701030	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
6	nsv897706	chr11:64591679-64721908	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
7	nsv897707	chr11:64600002-64701030	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
8	nsv897708	chr11:64602757-64695271	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
9	nsv360	chr11:64632395-64659636	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1003 gene(s)	inside rSNPs	diseases
10	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
11	nsv555208	chr11:64645119-64771179	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1029 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs602347	EHD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64646400-64648600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr11:64646400-64648600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
3	chr11:64646400-64648600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr11:64646600-64648400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
5	chr11:64646600-64648600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr11:64646800-64648600	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr11:64646800-64648600	Flanking Active TSS	GM12878-XiMat	blood
8	chr11:64647000-64648200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:64647000-64648200	Enhancers	Stomach Mucosa	stomach
10	chr11:64647000-64648400	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr11:64647000-64648600	Enhancers	Brain Cingulate Gyrus	brain
12	chr11:64647000-64648600	Enhancers	Fetal Muscle Leg	muscle
13	chr11:64647000-64648600	Enhancers	Small Intestine	intestine
14	chr11:64647000-64649000	Enhancers	Primary B cells from peripheral blood	blood
15	chr11:64647000-64649600	Enhancers	Placenta	Placenta
16	chr11:64647000-64655200	Weak transcription	Esophagus	oesophagus
17	chr11:64647000-64655400	Weak transcription	Ovary	ovary
18	chr11:64647200-64648200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr11:64647200-64648200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr11:64647200-64648200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr11:64647200-64648200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:64647200-64648200	Enhancers	Colonic Mucosa	Colon
23	chr11:64647200-64648400	Weak transcription	Right Atrium	heart
24	chr11:64647200-64648400	Enhancers	NHLF	lung
25	chr11:64647200-64648400	Enhancers	Osteobl	bone
26	chr11:64647200-64648600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:64647200-64648600	Enhancers	Brain Hippocampus Middle	brain
28	chr11:64647200-64648600	Enhancers	Brain Substantia Nigra	brain
29	chr11:64647200-64648800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr11:64647200-64648800	Enhancers	Liver	Liver
31	chr11:64647200-64648800	Enhancers	Fetal Intestine Small	intestine
32	chr11:64647200-64649000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:64647200-64649200	Enhancers	Fetal Muscle Trunk	muscle
34	chr11:64647200-64649200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr11:64647200-64649400	Enhancers	Fetal Thymus	thymus
36	chr11:64647200-64649600	Enhancers	Fetal Intestine Large	intestine
37	chr11:64647200-64649600	Enhancers	NHDF-Ad	bronchial
38	chr11:64647200-64649800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr11:64647200-64650800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:64647200-64652600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr11:64647200-64653000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr11:64647200-64653000	Weak transcription	HMEC	breast
43	chr11:64647200-64655000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:64647200-64655600	Weak transcription	Gastric	stomach
45	chr11:64647400-64648200	Enhancers	Brain Anterior Caudate	brain
46	chr11:64647400-64648400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:64647400-64648400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr11:64647400-64648400	Enhancers	HepG2	liver
49	chr11:64647400-64648400	Enhancers	K562	blood
50	chr11:64647400-64648600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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