Variant report

Variant	rs9991944
Chromosome Location	chr4:166246496-166246497
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	POLR2A	chr4:166246475-166247352	GM12892	blood:	n/a	n/a
2	GATA3	chr4:166246171-166246817	MCF-7	breast:	n/a	n/a
3	MAFF	chr4:166246076-166246547	K562	blood:	n/a	chr4:166246254-166246268 chr4:166246255-166246273
4	POLR2A	chr4:166246495-166247678	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr4:166246470-166247660	HCT-116	colon:	n/a	n/a
6	GATA1	chr4:166246030-166247702	PBDE	blood:	n/a	n/a
7	JUN	chr4:166245200-166249708	K562	blood:	n/a	chr4:166248765-166248774 chr4:166248995-166249004
8	RCOR1	chr4:166246396-166246757	K562	blood:	n/a	n/a
9	POLR2A	chr4:166246445-166267299	K562	blood:	n/a	n/a
10	RCOR1	chr4:166246261-166247869	K562	blood:	n/a	n/a
11	CBX3	chr4:166246426-166247773	HCT-116	colon:	n/a	n/a
12	MAFK	chr4:166246079-166246502	IMR90	lung:	n/a	chr4:166246254-166246268 chr4:166246253-166246269 chr4:166246261-166246272 chr4:166246259-166246273 chr4:166246260-166246271 chr4:166246256-166246272 chr4:166246256-166246271 chr4:166246261-166246272 chr4:166246251-166246271 chr4:166246260-166246271
13	POLR2A	chr4:166246431-166249506	IMR90	lung:	n/a	n/a
14	MAFK	chr4:166245706-166247638	K562	blood:	n/a	chr4:166246254-166246268 chr4:166246253-166246269 chr4:166246261-166246272 chr4:166246259-166246273 chr4:166245843-166245858 chr4:166246260-166246271 chr4:166246256-166246272 chr4:166246256-166246271 chr4:166246261-166246272 chr4:166246251-166246271 chr4:166246260-166246271
15	POLR2A	chr4:166245882-166247263	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:166128531..166130929-chr4:166246215..166249595,5	MCF-7	breast:

Variant related genes	Relation type
MSMO1	TF binding region
ENSG00000109466	Chromatin interaction
ENSG00000170088	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10010264	1.00[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs10019675	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs10022944	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs10031749	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs12108624	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap]
rs12330937	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs28495546	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs28520278	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs28525405	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs28641126	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs28853353	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap]
rs57823891	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834112	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7665057	0.83[AMR][1000 genomes]
rs9999376	0.86[JPT][hapmap]

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	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166214400-166246600	Weak transcription	Placenta	Placenta
2	chr4:166219400-166246600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr4:166219400-166246600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:166219600-166246800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:166220000-166246600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:166220000-166247000	Weak transcription	Spleen	Spleen
7	chr4:166220000-166247400	Weak transcription	Fetal Stomach	stomach
8	chr4:166220000-166247800	Weak transcription	Right Ventricle	heart
9	chr4:166223400-166246600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:166223400-166246600	Weak transcription	Esophagus	oesophagus
11	chr4:166223400-166246600	Weak transcription	HSMM	muscle
12	chr4:166223400-166246600	Weak transcription	HSMMtube	muscle
13	chr4:166223400-166246800	Weak transcription	Ovary	ovary
14	chr4:166223400-166247400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:166223400-166247600	Weak transcription	Thymus	Thymus
16	chr4:166223400-166247800	Weak transcription	Aorta	Aorta
17	chr4:166223400-166248000	Weak transcription	Gastric	stomach
18	chr4:166223600-166246600	Weak transcription	GM12878-XiMat	blood
19	chr4:166223600-166247000	Weak transcription	Brain Anterior Caudate	brain
20	chr4:166223600-166247200	Weak transcription	Brain Angular Gyrus	brain
21	chr4:166223600-166247200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:166223600-166247400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:166223600-166247400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr4:166223600-166247600	Weak transcription	Fetal Lung	lung
25	chr4:166223800-166247600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:166224200-166247400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:166224200-166247600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:166224400-166247600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:166230800-166246600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:166230800-166246800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr4:166230800-166247000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:166230800-166247400	Weak transcription	Brain Germinal Matrix	brain
33	chr4:166230800-166247400	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:166231800-166246800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:166232000-166246600	Weak transcription	NH-A	brain
36	chr4:166232000-166247200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr4:166232000-166247200	Weak transcription	Brain Substantia Nigra	brain
38	chr4:166232800-166247200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr4:166233000-166248000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr4:166233400-166246600	Weak transcription	Pancreas	Pancrea
41	chr4:166233400-166247000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:166233400-166247200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:166233400-166247600	Weak transcription	Adipose Nuclei	Adipose
44	chr4:166233400-166247800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:166233400-166248000	Weak transcription	Left Ventricle	heart
46	chr4:166233800-166246600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:166234000-166247200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr4:166234000-166247600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:166234200-166246800	Weak transcription	NHDF-Ad	bronchial
50	chr4:166234400-166246600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links