Variant report

Variant	rs9401092
Chromosome Location	chr6:119216729-119216730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:119214267-119216784	Hela-S3	cervix:	n/a	n/a
2	NRF1	chr6:119216007-119216732	SK-N-SH	brain:	n/a	chr6:119216177-119216186
3	POLR2A	chr6:119215886-119216817	IMR90	lung:	n/a	n/a
4	POLR2A	chr6:119214645-119216729	K562	blood:	n/a	n/a
5	POLR2A	chr6:119214360-119216740	HL-60	blood:	n/a	n/a
6	POLR2A	chr6:119214110-119216820	U87	brain:	n/a	n/a
7	HA-E2F1	chr6:119214663-119216780	MCF-7	breast:	n/a	chr6:119216174-119216183 chr6:119216016-119216025
8	POLR2A	chr6:119214110-119216785	U87	brain:	n/a	n/a
9	MXI1	chr6:119214300-119216826	IMR90	lung:	n/a	n/a
10	MYC	chr6:119216670-119217225	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr6:119214152-119216764	HUVEC	blood vessel:	n/a	n/a
12	SIN3A	chr6:119214327-119216856	H1-hESC	embryonic stem cell:	n/a	chr6:119216419-119216432
13	RCOR1	chr6:119213939-119216809	IMR90	lung:	n/a	n/a
14	POLR2A	chr6:119214936-119216740	HUVEC	blood vessel:	n/a	n/a
15	CHD1	chr6:119213402-119216846	IMR90	lung:	n/a	n/a
16	CHD1	chr6:119214496-119217944	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr6:119214790-119217179	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr6:119214027-119216777	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr6:119214479-119216788	Hela-S3	cervix:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:119214552..119219906-chr6:119253918..119257622,8	MCF-7	breast:
2	chr6:119216722..119218492-chr6:119251658..119253168,2	K562	blood:
3	chr6:119213105..119220728-chr6:119253299..119257962,22	K562	blood:
4	chr6:119213036..119217484-chr6:119254311..119257675,9	MCF-7	breast:
5	chr6:119213694..119219544-chr6:119251621..119258172,21	K562	blood:
6	chr6:119030681..119033583-chr6:119216548..119219009,2	K562	blood:
7	chr6:119215906..119219234-chr6:119443291..119446175,3	K562	blood:
8	chr5:140698166..140700662-chr6:119215254..119217886,2	MCF-7	breast:
9	chr6:119215924..119218586-chr6:119236069..119238504,2	K562	blood:
10	chr6:119213805..119216904-chr6:119398441..119401842,5	K562	blood:
11	chr6:118997357..119000224-chr6:119215620..119217691,2	K562	blood:
12	chr6:119027193..119028788-chr6:119215908..119217917,2	K562	blood:
13	chr6:119029203..119032181-chr6:119214720..119218048,3	K562	blood:
14	chr6:119215862..119217383-chr6:119670691..119672707,2	K562	blood:
15	chr6:119216161..119219506-chr6:119398191..119401599,4	K562	blood:

No data

Variant related genes	Relation type
MCM9	TF binding region
ENSG00000253194	Chromatin interaction
ENSG00000111879	Chromatin interaction
ENSG00000111877	Chromatin interaction
ENSG00000111860	Chromatin interaction
ENSG00000178913	Chromatin interaction
ENSG00000255729	Chromatin interaction
ENSG00000111885	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11153781	0.91[ASN][1000 genomes]
rs11153791	0.95[ASN][1000 genomes]
rs12207663	0.95[ASN][1000 genomes]
rs12213327	0.95[ASN][1000 genomes]
rs4343954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61299241	1.00[AMR][1000 genomes]
rs67182660	1.00[ASN][1000 genomes]
rs6902942	0.95[ASN][1000 genomes]
rs7775275	1.00[ASN][1000 genomes]
rs9372515	0.85[AMR][1000 genomes]
rs9372521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9374756	1.00[ASN][1000 genomes]
rs9374760	0.95[ASN][1000 genomes]
rs9374762	0.95[ASN][1000 genomes]
rs9374769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9374770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9385059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9385066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9387602	0.85[AMR][1000 genomes]
rs9387607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9387618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9387623	1.00[AMR][1000 genomes]
rs9387627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9401094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9401095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9401096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9401100	0.95[ASN][1000 genomes]
rs9401101	0.95[ASN][1000 genomes]
rs9401110	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9401111	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9401112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9401117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023826	chr6:119026481-119221408	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119213400-119217800	Active TSS	Right Atrium	heart
2	chr6:119213600-119216800	Active TSS	Colonic Mucosa	Colon
3	chr6:119213600-119216800	Active TSS	Psoas Muscle	Psoas
4	chr6:119213600-119217000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:119213600-119217600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:119213600-119217800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:119213600-119218000	Active TSS	Primary T cells fromperipheralblood	blood
8	chr6:119213600-119218200	Active TSS	NHLF	lung
9	chr6:119213800-119216800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:119213800-119216800	Active TSS	Aorta	Aorta
11	chr6:119213800-119216800	Active TSS	Brain Angular Gyrus	brain
12	chr6:119213800-119216800	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr6:119213800-119216800	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr6:119213800-119217000	Active TSS	Fetal Muscle Leg	muscle
15	chr6:119213800-119217600	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:119213800-119217600	Active TSS	Fetal Thymus	thymus
17	chr6:119213800-119217600	Active TSS	HSMMtube	muscle
18	chr6:119213800-119218000	Active TSS	GM12878-XiMat	blood
19	chr6:119213800-119218200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr6:119214000-119216800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:119214000-119216800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr6:119214000-119216800	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr6:119214000-119216800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:119214000-119216800	Active TSS	Brain Substantia Nigra	brain
25	chr6:119214000-119216800	Active TSS	Fetal Intestine Small	intestine
26	chr6:119214000-119216800	Active TSS	Fetal Muscle Trunk	muscle
27	chr6:119214000-119216800	Active TSS	Placenta	Placenta
28	chr6:119214000-119216800	Active TSS	Rectal Smooth Muscle	rectum
29	chr6:119214000-119216800	Active TSS	HSMM	muscle
30	chr6:119214000-119217000	Active TSS	Fetal Intestine Large	intestine
31	chr6:119214000-119217000	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr6:119214000-119217000	Active TSS	Fetal Stomach	stomach
33	chr6:119214000-119217000	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr6:119214000-119217000	Active TSS	Stomach Smooth Muscle	stomach
35	chr6:119214000-119217000	Active TSS	NHDF-Ad	bronchial
36	chr6:119214000-119217200	Active TSS	NHEK	skin
37	chr6:119214000-119217400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:119214000-119217400	Active TSS	Brain Anterior Caudate	brain
39	chr6:119214000-119217400	Active TSS	Brain Cingulate Gyrus	brain
40	chr6:119214000-119217400	Active TSS	Thymus	Thymus
41	chr6:119214000-119217600	Active TSS	Fetal Brain Female	brain
42	chr6:119214000-119217800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:119214000-119218000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:119214000-119218000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:119214200-119216800	Active TSS	Brain Hippocampus Middle	brain
46	chr6:119214200-119216800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr6:119214200-119216800	Active TSS	Fetal Heart	heart
48	chr6:119214200-119216800	Active TSS	Ovary	ovary
49	chr6:119214200-119216800	Active TSS	Right Ventricle	heart
50	chr6:119214200-119217000	Active TSS	iPS-15b Cell Line	embryonic stem cell

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