Variant report

Variant	rs61782162
Chromosome Location	chr1:94345619-94345620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:94344153-94345721	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:94344000-94345721	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:94344078-94345860	SK-N-MC	brain:	n/a	n/a
4	BCL3	chr1:94343887-94345861	A549	lung:	n/a	n/a
5	POLR2A	chr1:94344025-94345752	GM12891	blood:	n/a	n/a
6	POLR2A	chr1:94344157-94346337	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:94345383-94345864	PFSK-1	brain:	n/a	n/a
8	HCFC1	chr1:94343782-94345845	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:94344028-94345736	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:94343867-94345668	K562	blood:	n/a	n/a
11	MXI1	chr1:94343607-94345758	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr1:94343911-94345636	IMR90	lung:	n/a	n/a
13	BCL3	chr1:94345311-94345824	A549	lung:	n/a	n/a
14	POLR2A	chr1:94343945-94345667	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:94345497-94345673	K562	blood:	n/a	n/a
16	POLR2A	chr1:94343685-94350802	A549	lung:	n/a	n/a
17	POLR2A	chr1:94344063-94345687	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr1:94344399-94345803	SK-N-SH	brain:	n/a	n/a
19	REST	chr1:94344096-94345671	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr1:94344319-94345628	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:94343810-94352873	K562	blood:	n/a	n/a
22	POLR2A	chr1:94343890-94345740	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr1:94343980-94345641	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:94336837..94340766-chr1:94341847..94346212,6	K562	blood:
2	chr1:94343199..94347658-chr1:94372955..94376562,9	MCF-7	breast:
3	chr1:94337347..94339597-chr1:94344098..94346567,2	MCF-7	breast:
4	chr1:94344690..94346304-chr1:94373768..94376372,3	MCF-7	breast:
5	chr1:94311992..94315197-chr1:94341852..94346150,3	MCF-7	breast:
6	chr1:94344173..94346291-chr1:94372636..94375124,3	K562	blood:
7	chr1:94342014..94348814-chr1:94369991..94376733,14	K562	blood:
8	chr1:94310839..94314732-chr1:94343365..94346802,6	MCF-7	breast:
9	chr1:94310214..94315053-chr1:94342432..94346579,12	K562	blood:

No data

Variant related genes	Relation type
DNTTIP2	TF binding region
ENSG00000023909	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000067334	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10489605	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10874795	0.81[ASN][1000 genomes]
rs11164994	0.90[EUR][1000 genomes]
rs11165019	0.81[ASN][1000 genomes]
rs12079584	0.81[ASN][1000 genomes]
rs12239830	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17100397	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17304770	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17878271	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17878294	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17881810	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17884788	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17885151	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17886352	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877605	0.82[EUR][1000 genomes]
rs2223908	0.92[EUR][1000 genomes]
rs3761913	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292665	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57870303	0.90[EUR][1000 genomes]
rs61425457	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61781049	0.88[EUR][1000 genomes]
rs61781051	0.90[EUR][1000 genomes]
rs61781053	0.92[EUR][1000 genomes]
rs61781054	0.90[EUR][1000 genomes]
rs61781055	0.90[EUR][1000 genomes]
rs61781056	0.90[EUR][1000 genomes]
rs61781057	0.92[EUR][1000 genomes]
rs61782163	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782164	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782165	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782167	0.86[ASN][1000 genomes]
rs61782398	0.90[EUR][1000 genomes]
rs61782399	0.90[EUR][1000 genomes]
rs61782400	0.92[EUR][1000 genomes]
rs61782403	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782404	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782405	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782410	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782413	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782449	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61782450	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782451	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61782458	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782459	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674149	0.85[EUR][1000 genomes]
rs72723114	0.90[EUR][1000 genomes]
rs72723118	0.92[EUR][1000 genomes]
rs72723125	0.92[EUR][1000 genomes]
rs72723138	0.90[EUR][1000 genomes]
rs72723157	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72723165	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72723169	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72723178	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723192	0.94[ASN][1000 genomes]
rs72967397	0.81[ASN][1000 genomes]
rs7523682	0.88[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61782162	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94342800-94345800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:94343400-94345800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:94343400-94345800	Active TSS	A549	lung
4	chr1:94343800-94345800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:94343800-94345800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:94344400-94345800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:94344400-94345800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:94345000-94357000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:94345000-94374200	Weak transcription	Gastric	stomach
10	chr1:94345000-94374200	Weak transcription	Spleen	Spleen
11	chr1:94345200-94345800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:94345200-94345800	Flanking Active TSS	Dnd41	blood
13	chr1:94345200-94358800	Weak transcription	Left Ventricle	heart
14	chr1:94345200-94374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:94345200-94374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:94345400-94345800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:94345400-94345800	Enhancers	Primary T cells from cord blood	blood
18	chr1:94345400-94345800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:94345400-94345800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:94345400-94346400	Weak transcription	HSMM	muscle
21	chr1:94345400-94348600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:94345400-94353600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:94345400-94353600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:94345400-94353600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:94345400-94354400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:94345400-94356600	Weak transcription	Aorta	Aorta
27	chr1:94345400-94356800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:94345400-94357000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:94345400-94357200	Weak transcription	NHLF	lung
30	chr1:94345400-94358800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:94345400-94359200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:94345400-94361000	Weak transcription	Fetal Thymus	thymus
33	chr1:94345400-94362000	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:94345400-94364000	Weak transcription	Fetal Intestine Small	intestine
35	chr1:94345400-94369400	Weak transcription	Colonic Mucosa	Colon
36	chr1:94345400-94373200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:94345400-94373200	Weak transcription	Brain Substantia Nigra	brain
38	chr1:94345400-94373800	Weak transcription	Fetal Stomach	stomach
39	chr1:94345400-94374000	Weak transcription	Right Ventricle	heart
40	chr1:94345600-94345800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:94345600-94345800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr1:94345600-94345800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr1:94345600-94345800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr1:94345600-94345800	Enhancers	Fetal Heart	heart
45	chr1:94345600-94345800	Flanking Active TSS	HMEC	breast
46	chr1:94345600-94345800	Enhancers	HSMMtube	muscle
47	chr1:94345600-94346800	Enhancers	Osteobl	bone
48	chr1:94345600-94347600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:94345600-94347600	Weak transcription	HUVEC	blood vessel
50	chr1:94345600-94347800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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