Variant report

Variant	rs4340549
Chromosome Location	chr2:191333728-191333729
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	EP300	chr2:191333368-191335652	SK-N-SH	brain:	n/a	n/a
2	KAP1	chr2:191333573-191334289	U2OS	brain:	n/a	n/a
3	KAP1	chr2:191333489-191334329	HEK293	kidney:	n/a	n/a
4	TCF12	chr2:191333384-191334442	SK-N-SH	brain:	n/a	chr2:191334032-191334041 chr2:191333849-191333858
5	GATA3	chr2:191333715-191334409	MCF-7	breast:	n/a	n/a
6	GATA3	chr2:191333609-191334446	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr2:191333596-191334215	ECC-1	luminal epithelium:	n/a	chr2:191334032-191334041 chr2:191333849-191333858
8	NFIC	chr2:191333584-191334399	SK-N-SH	brain:	n/a	n/a
9	EP300	chr2:191333423-191334465	SK-N-SH	brain:	n/a	n/a
10	NFIC	chr2:191333380-191334410	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr2:191333537-191334312	GM12878	blood:	n/a	n/a
12	GATA2	chr2:191333660-191335523	SH-SY5Y	brain:	n/a	n/a
13	GATA3	chr2:191333433-191334958	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr2:191333716-191335411	MCF10A-Er-Src	breast:	n/a	n/a
15	NFIC	chr2:191333379-191335520	SK-N-SH	brain:	n/a	n/a
16	SIN3AK20	chr2:191333683-191334884	MCF-7	breast:	n/a	n/a
17	NFIC	chr2:191333395-191334437	ECC-1	luminal epithelium:	n/a	n/a
18	RCOR1	chr2:191333137-191334443	IMR90	lung:	n/a	n/a
19	RAD21	chr2:191333692-191334328	IMR90	lung:	n/a	n/a
20	MYC	chr2:191333651-191334239	K562	blood:	n/a	n/a
21	TCF12	chr2:191333453-191334463	SK-N-SH	brain:	n/a	chr2:191334032-191334041 chr2:191333849-191333858
22	SETDB1	chr2:191333661-191334186	U2OS	brain:	n/a	n/a
23	FOXP2	chr2:191333627-191333855	SK-N-MC	brain:	n/a	n/a
24	SP1	chr2:191333692-191334392	A549	lung:	n/a	chr2:191334059-191334072
25	TCF12	chr2:191333517-191335063	A549	lung:	n/a	chr2:191334032-191334041 chr2:191333849-191333858
26	MAZ	chr2:191333686-191333802	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:191318515..191323057-chr2:191332501..191335066,4	MCF-7	breast:
2	chr2:191272262..191274939-chr2:191333629..191335814,2	MCF-7	breast:
3	chr2:191271631..191274450-chr2:191332507..191334267,2	MCF-7	breast:
4	chr2:191332610..191334392-chr2:191512174..191513999,2	K562	blood:

Variant related genes	Relation type
MFSD6	TF binding region
ENSG00000272979	Chromatin interaction
ENSG00000151690	Chromatin interaction
ENSG00000138386	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10084203	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10174174	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10188341	0.84[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10190082	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193212	0.85[LWK][hapmap]
rs10197348	0.83[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10432434	0.98[ASN][1000 genomes]
rs10931458	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128723	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11885992	0.98[ASN][1000 genomes]
rs12052514	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12053190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12470863	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12472081	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12477369	0.80[ASN][1000 genomes]
rs12613807	0.85[LWK][hapmap]
rs12693579	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13409841	0.83[LWK][hapmap]
rs13417431	0.80[ASN][1000 genomes]
rs16832765	0.90[JPT][hapmap]
rs2192010	0.80[ASN][1000 genomes]
rs35818159	0.95[ASN][1000 genomes]
rs4129082	0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4258824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4261750	0.81[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4287794	0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4371384	0.93[ASN][1000 genomes]
rs4439990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4641969	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853510	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853710	0.81[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4853711	0.81[AFR][1000 genomes]
rs4853713	0.89[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs4853716	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56342910	0.84[ASN][1000 genomes]
rs59929070	0.86[ASN][1000 genomes]
rs60847675	0.83[EUR][1000 genomes]
rs60915953	0.98[ASN][1000 genomes]
rs61709084	0.80[ASN][1000 genomes]
rs62180992	0.80[ASN][1000 genomes]
rs62181018	0.86[ASN][1000 genomes]
rs62181019	0.86[ASN][1000 genomes]
rs62181020	0.86[ASN][1000 genomes]
rs62181029	0.97[ASN][1000 genomes]
rs62181034	0.98[ASN][1000 genomes]
rs62181052	0.97[ASN][1000 genomes]
rs62182865	0.93[ASN][1000 genomes]
rs6711928	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6712426	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6727669	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6731287	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567059	0.98[ASN][1000 genomes]
rs7569128	0.90[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7581762	0.81[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7581986	0.81[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7593240	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33134	chr2:191318791-191365710	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4340549	INPP1	cis	parietal	SCAN
rs4340549	INPP1	cis	cerebellum	SCAN
rs4340549	INPP1	Cis_1M	lymphoblastoid	RTeQTL
rs4340549	MFSD6	cis	cerebellum	SCAN
rs4340549	HIBCH	cis	parietal	SCAN
rs4340549	MSTN	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191306600-191351000	Weak transcription	Pancreas	Pancrea
2	chr2:191322000-191335800	Weak transcription	Esophagus	oesophagus
3	chr2:191322600-191335600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:191323000-191334600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:191323200-191335800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:191325600-191335800	Weak transcription	Lung	lung
7	chr2:191325600-191346200	Weak transcription	Right Ventricle	heart
8	chr2:191327600-191353000	Weak transcription	Primary B cells from cord blood	blood
9	chr2:191328800-191334400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr2:191328800-191334600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:191329600-191334600	Weak transcription	Thymus	Thymus
12	chr2:191330000-191334800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:191330200-191334800	Enhancers	K562	blood
14	chr2:191330600-191335200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:191330800-191333800	Enhancers	Brain Hippocampus Middle	brain
16	chr2:191330800-191334800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:191330800-191335400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:191330800-191335400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:191331000-191334400	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr2:191331000-191334800	Enhancers	NHDF-Ad	bronchial
21	chr2:191331000-191335000	Enhancers	Brain Substantia Nigra	brain
22	chr2:191331000-191335200	Enhancers	Brain Cingulate Gyrus	brain
23	chr2:191331000-191335400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:191331000-191335400	Enhancers	Hela-S3	cervix
25	chr2:191331000-191335400	Enhancers	Osteobl	bone
26	chr2:191331200-191335400	Enhancers	NHLF	lung
27	chr2:191331200-191335600	Enhancers	Fetal Lung	lung
28	chr2:191331400-191333800	Enhancers	Right Atrium	heart
29	chr2:191331400-191333800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr2:191331400-191334200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr2:191331400-191334400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr2:191331400-191334400	Enhancers	Fetal Brain Male	brain
33	chr2:191331400-191334800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:191331400-191334800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:191331400-191335000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr2:191331400-191335000	Enhancers	Rectal Smooth Muscle	rectum
37	chr2:191331400-191335200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:191331400-191335200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:191331400-191335400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:191331400-191335400	Enhancers	Brain Angular Gyrus	brain
41	chr2:191331400-191335400	Enhancers	Fetal Heart	heart
42	chr2:191331400-191335400	Enhancers	Fetal Muscle Leg	muscle
43	chr2:191331400-191335400	Enhancers	Fetal Stomach	stomach
44	chr2:191331400-191335600	Enhancers	Colon Smooth Muscle	Colon
45	chr2:191331600-191333800	Enhancers	Left Ventricle	heart
46	chr2:191331600-191334200	Enhancers	Fetal Brain Female	brain
47	chr2:191331600-191334400	Enhancers	Adipose Nuclei	Adipose
48	chr2:191331600-191334600	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr2:191331600-191334800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:191331600-191334800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links