Variant report

Variant	rs7772912
Chromosome Location	chr6:119218470-119218471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr6:119218433-119218507	K562	blood:	n/a	n/a
2	POLR2A	chr6:119217320-119218549	K562	blood:	n/a	n/a
3	POLR2A	chr6:119217437-119218517	HepG2	liver:	n/a	n/a

No data

(count:10 , 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	chr6:119213694..119219544-chr6:119251621..119258172,21	K562	blood:
5	chr6:119030681..119033583-chr6:119216548..119219009,2	K562	blood:
6	chr6:119215906..119219234-chr6:119443291..119446175,3	K562	blood:
7	chr6:119217885..119221356-chr6:119243903..119247955,3	K562	blood:
8	chr6:119215924..119218586-chr6:119236069..119238504,2	K562	blood:
9	chr6:119217885..119219986-chr6:119244920..119246613,2	K562	blood:
10	chr6:119216161..119219506-chr6:119398191..119401599,4	K562	blood:

No data

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

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10456918	0.97[EUR][1000 genomes]
rs1068588	0.81[EUR][1000 genomes]
rs11153777	0.89[EUR][1000 genomes]
rs11153778	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs11153780	0.97[EUR][1000 genomes]
rs11153781	0.81[EUR][1000 genomes]
rs11153791	0.95[EUR][1000 genomes]
rs12190099	0.89[EUR][1000 genomes]
rs12202077	0.87[EUR][1000 genomes]
rs12204084	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12204825	0.94[EUR][1000 genomes]
rs12207663	0.95[EUR][1000 genomes]
rs12211725	0.83[EUR][1000 genomes]
rs12213327	0.95[EUR][1000 genomes]
rs12213597	0.83[EUR][1000 genomes]
rs17506361	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1775617	0.84[EUR][1000 genomes]
rs2295709	0.86[CEU][hapmap]
rs284919	0.82[CEU][hapmap]
rs590004	0.81[EUR][1000 genomes]
rs610960	0.81[EUR][1000 genomes]
rs639266	0.80[EUR][1000 genomes]
rs669978	0.81[EUR][1000 genomes]
rs67182660	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6902942	0.95[EUR][1000 genomes]
rs7740819	0.83[EUR][1000 genomes]
rs7750373	0.81[EUR][1000 genomes]
rs7771525	0.85[EUR][1000 genomes]
rs7775251	0.83[EUR][1000 genomes]
rs7775275	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs794614	0.86[CEU][hapmap]
rs813233	0.81[EUR][1000 genomes]
rs9374756	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9374760	0.95[EUR][1000 genomes]
rs9374762	0.95[EUR][1000 genomes]
rs9374774	0.83[EUR][1000 genomes]
rs9387618	1.00[CHB][hapmap]
rs9387631	0.83[EUR][1000 genomes]
rs9401101	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7772912	BRD7P3	cis	parietal	SCAN
rs7772912	MCM9	cis	cerebellum	SCAN
rs7772912	MCM9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119216600-119219600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:119216600-119220200	Weak transcription	Pancreas	Pancrea
3	chr6:119216600-119220200	Weak transcription	Spleen	Spleen
4	chr6:119216600-119220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:119216600-119220400	Weak transcription	Esophagus	oesophagus
6	chr6:119216600-119224400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:119216600-119233800	Weak transcription	Lung	lung
8	chr6:119216600-119236600	Weak transcription	Gastric	stomach
9	chr6:119216600-119243800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:119216800-119218600	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:119216800-119219200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:119216800-119219200	Weak transcription	Placenta	Placenta
13	chr6:119216800-119219600	Weak transcription	HSMM	muscle
14	chr6:119216800-119220200	Weak transcription	Right Ventricle	heart
15	chr6:119216800-119230600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:119216800-119232400	Weak transcription	Colonic Mucosa	Colon
17	chr6:119216800-119232600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:119216800-119233200	Weak transcription	Aorta	Aorta
19	chr6:119216800-119235800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:119217000-119218600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:119217000-119220200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:119217000-119223200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:119217000-119225400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:119217000-119242200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:119217200-119219400	Enhancers	Colon Smooth Muscle	Colon
26	chr6:119217400-119219000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:119217600-119218600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:119217600-119218600	Enhancers	Small Intestine	intestine
29	chr6:119217600-119219200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:119217600-119220200	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:119217600-119221600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:119217600-119221800	Enhancers	Ovary	ovary
33	chr6:119217600-119222600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr6:119217800-119218600	Genic enhancers	Fetal Thymus	thymus
35	chr6:119217800-119218800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:119217800-119219000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:119217800-119219000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr6:119217800-119219000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:119217800-119219000	Weak transcription	Fetal Heart	heart
40	chr6:119217800-119219000	Weak transcription	A549	lung
41	chr6:119217800-119219000	Enhancers	NH-A	brain
42	chr6:119217800-119219200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:119217800-119219200	Enhancers	Fetal Lung	lung
44	chr6:119217800-119219200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr6:119217800-119219400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:119217800-119219600	Weak transcription	Fetal Stomach	stomach
47	chr6:119217800-119219800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:119217800-119219800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr6:119217800-119219800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:119217800-119219800	Weak transcription	Fetal Intestine Large	intestine

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