Variant report

Variant	rs7518016
Chromosome Location	chr1:150122890-150122891
allele	A/G
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	CHD1	chr1:150120708-150124616	IMR90	lung:	n/a	chr1:150122211-150122221
2	TAF1	chr1:150122832-150123039	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:150121015-150124391	HUVEC	blood vessel:	n/a	n/a
4	MAZ	chr1:150121633-150123091	K562	blood:	n/a	n/a
5	TBL1XR1	chr1:150122854-150123040	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:150122855-150124712	GM12891	blood:	n/a	n/a
7	ZBTB7A	chr1:150121570-150123173	ECC-1	luminal epithelium:	n/a	chr1:150122209-150122216
8	POLR2A	chr1:150122828-150124645	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr1:150122830-150124656	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:150122718-150123058	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3A	chr1:150122836-150123254	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr1:150120907-150124920	IMR90	lung:	n/a	n/a
13	POLR2A	chr1:150120758-150124804	GM12892	blood:	n/a	n/a
14	POLR2A	chr1:150121688-150124546	IMR90	lung:	n/a	n/a
15	POLR2A	chr1:150121557-150124225	GM18951	blood:	n/a	n/a
16	EGR1	chr1:150121297-150122894	MCF-7	breast:	n/a	chr1:150121993-150122003 chr1:150121992-150122007 chr1:150122224-150122233 chr1:150122506-150122516 chr1:150121993-150122006 chr1:150121998-150122008 chr1:150121993-150122006 chr1:150121997-150122007 chr1:150121724-150121734
17	RUNX3	chr1:150122862-150123241	GM12878	blood:	n/a	n/a
18	ZBTB7A	chr1:150121640-150123226	ECC-1	luminal epithelium:	n/a	chr1:150122209-150122216
19	POLR2A	chr1:150121538-150122996	HUVEC	blood vessel:	n/a	n/a
20	CHD1	chr1:150122234-150124524	GM12878	blood:	n/a	n/a
21	BACH1	chr1:150122636-150122999	H1-hESC	embryonic stem cell:	n/a	n/a
22	UBTF	chr1:150122731-150123188	K562	blood:	n/a	n/a
23	POLR2A	chr1:150121723-150123177	K562	blood:	n/a	n/a
24	CHD1	chr1:150122789-150123205	H1-hESC	embryonic stem cell:	n/a	n/a
25	TAF1	chr1:150122647-150123199	H1-neurons	neurons:	n/a	n/a
26	POLR2A	chr1:150120703-150124835	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:150120919-150124258	H1-neurons	neurons:	n/a	n/a
28	MAZ	chr1:150120991-150124771	IMR90	lung:	n/a	n/a
29	ZBTB7A	chr1:150121582-150123097	K562	blood:	n/a	chr1:150122209-150122216
30	RAD21	chr1:150122793-150123375	IMR90	lung:	n/a	n/a
31	EGR1	chr1:150121860-150123071	K562	blood:	n/a	chr1:150121993-150122003 chr1:150121992-150122007 chr1:150122224-150122233 chr1:150122506-150122516 chr1:150121993-150122006 chr1:150121998-150122008 chr1:150121993-150122006 chr1:150121997-150122007
32	SPI1	chr1:150122842-150123253	HL-60	blood:	n/a	n/a
33	TAF1	chr1:150122612-150123437	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr1:150122567-150124789	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:150121634-150124231	GM18526	blood:	n/a	n/a
36	TAF1	chr1:150122601-150123320	H1-neurons	neurons:	n/a	n/a
37	ZBTB7A	chr1:150122774-150122921	HepG2	liver:	n/a	n/a
38	POLR2A	chr1:150121054-150124276	GM19099	blood:	n/a	n/a
39	FOXA1	chr1:150122606-150122987	HepG2	liver:	n/a	chr1:150122639-150122651
40	POLR2A	chr1:150122674-150136351	U87	brain:	n/a	n/a
41	POLR2A	chr1:150122674-150124654	U87	brain:	n/a	n/a
42	FOXA2	chr1:150122755-150123006	HepG2	liver:	n/a	n/a
43	UBTF	chr1:150121908-150123153	K562	blood:	n/a	n/a
44	REST	chr1:150122709-150123331	H1-neurons	neurons:	n/a	n/a
45	MAZ	chr1:150122727-150122983	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:150122630-150122945	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr1:150121523-150124023	GM12878	blood:	n/a	n/a
48	PML	chr1:150122715-150124616	GM12878	blood:	n/a	n/a
49	HMGN3	chr1:150121828-150123120	K562	blood:	n/a	n/a
50	ZBTB7A	chr1:150121677-150122911	K562	blood:	n/a	chr1:150122209-150122216

No.	Distal block	Cell Line	Cell type
1	chr1:150047834..150051741-chr1:150120632..150125901,6	MCF-7	breast:
2	chr1:150120783..150123550-chr1:150205612..150208208,2	K562	blood:
3	chr1:150120710..150123122-chr1:155106674..155108306,2	MCF-7	breast:
4	chr1:150048782..150051113-chr1:150122010..150123547,2	MCF-7	breast:
5	chr1:149858428..149861867-chr1:150121197..150123185,3	K562	blood:
6	chr1:150038076..150040720-chr1:150121290..150124944,3	K562	blood:
7	chr1:150063760..150067981-chr1:150120061..150123839,7	MCF-7	breast:
8	chr1:150121990..150123693-chr1:150240466..150243151,2	K562	blood:
9	chr1:149858884..149861217-chr1:150120977..150123082,2	MCF-7	breast:
10	chr1:149855859..149860778-chr1:150121854..150124549,4	MCF-7	breast:
11	chr1:149856777..149860438-chr1:150121197..150124713,4	K562	blood:
12	chr1:150121582..150124449-chr1:150206466..150208946,2	MCF-7	breast:
13	chr1:150121553..150123075-chr6:27798165..27799927,2	MCF-7	breast:
14	chr1:150121160..150123717-chr1:150206817..150209674,5	MCF-7	breast:
15	chr1:150038270..150039782-chr1:150120828..150123212,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS45-1	chr1:150122827-150123248	NONHSAT006272

Variant related genes	Relation type
PLEKHO1	TF binding region
ENSG00000118292	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000197914	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000117362	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs16833279	0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs16835153	1.00[AMR][1000 genomes]
rs16835982	1.00[AMR][1000 genomes]
rs57788184	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57819791	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58820446	1.00[AMR][1000 genomes]
rs58834873	1.00[AMR][1000 genomes]
rs59821426	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60109648	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60477778	1.00[AMR][1000 genomes]
rs60616215	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011248	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011320	1.00[AMR][1000 genomes]
rs73013116	1.00[AMR][1000 genomes]
rs73017005	1.00[AMR][1000 genomes]
rs73020880	1.00[AMR][1000 genomes]
rs7527755	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv535152	chr1:150120726-150143089	Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv3342683	chr1:150120853-150124201	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3409123	chr1:150121478-150123676	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150114800-150125200	Weak transcription	Hela-S3	cervix
2	chr1:150120200-150123200	Active TSS	Stomach Smooth Muscle	stomach
3	chr1:150120200-150124000	Active TSS	GM12878-XiMat	blood
4	chr1:150120800-150123400	Active TSS	Fetal Muscle Trunk	muscle
5	chr1:150120800-150124000	Active TSS	Aorta	Aorta
6	chr1:150120800-150124400	Active TSS	Brain Anterior Caudate	brain
7	chr1:150120800-150125200	Active TSS	Brain Hippocampus Middle	brain
8	chr1:150120800-150125200	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr1:150121000-150123000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
10	chr1:150121000-150123200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:150121000-150123200	Active TSS	Fetal Stomach	stomach
12	chr1:150121000-150123600	Active TSS	HSMMtube	muscle
13	chr1:150121000-150124000	Active TSS	Right Atrium	heart
14	chr1:150121000-150124200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:150121000-150124200	Active TSS	Fetal Kidney	kidney
16	chr1:150121000-150125000	Active TSS	Brain Angular Gyrus	brain
17	chr1:150121200-150123000	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:150121200-150123200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:150121200-150123600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:150121200-150123800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:150121200-150123800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:150121200-150123800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:150121200-150123800	Active TSS	Ovary	ovary
24	chr1:150121200-150124200	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:150121200-150124200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:150121200-150124400	Active TSS	Psoas Muscle	Psoas
27	chr1:150121200-150124800	Active TSS	Lung	lung
28	chr1:150121400-150123000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:150121400-150123200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:150121400-150123200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:150121400-150123200	Active TSS	Colon Smooth Muscle	Colon
32	chr1:150121400-150123200	Active TSS	Placenta Amnion	Placenta Amnion
33	chr1:150121400-150123400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:150121400-150123400	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr1:150121400-150123600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:150121400-150123800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:150121400-150123800	Active TSS	Thymus	Thymus
38	chr1:150121400-150123800	Active TSS	NHDF-Ad	bronchial
39	chr1:150121400-150124000	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr1:150121400-150124400	Active TSS	Brain Substantia Nigra	brain
41	chr1:150121400-150124600	Active TSS	Esophagus	oesophagus
42	chr1:150121400-150124600	Active TSS	Left Ventricle	heart
43	chr1:150121400-150125800	Active TSS	Right Ventricle	heart
44	chr1:150121600-150123000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:150121600-150123000	Active TSS	Fetal Muscle Leg	muscle
46	chr1:150121600-150123000	Active TSS	A549	lung
47	chr1:150121600-150123200	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr1:150121600-150123200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:150121600-150123200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:150121600-150123200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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