Variant report

Variant	rs17050918
Chromosome Location	chr3:50126599-50126600
allele	C/G
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	chr3:50126008-50128248	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:50126164-50127042	GM12878	blood:	n/a	n/a
3	YY1	chr3:50126086-50127195	GM12891	blood:	n/a	chr3:50126369-50126383 chr3:50126949-50126957 chr3:50126901-50126915 chr3:50126945-50126965 chr3:50126948-50126970 chr3:50126375-50126384
4	POLR2A	chr3:50126046-50127417	GM12891	blood:	n/a	n/a
5	REST	chr3:50126178-50126605	SK-N-SH	brain:	n/a	n/a
6	TBL1XR1	chr3:50126157-50126810	GM12878	blood:	n/a	n/a
7	TAF1	chr3:50126130-50126900	GM12892	blood:	n/a	n/a
8	YY1	chr3:50126174-50126997	K562	blood:	n/a	chr3:50126369-50126383 chr3:50126949-50126957 chr3:50126901-50126915 chr3:50126945-50126965 chr3:50126948-50126970 chr3:50126375-50126384
9	NFIC	chr3:50126581-50127204	GM12878	blood:	n/a	n/a
10	MYC	chr3:50126187-50127141	MCF-7	breast:	n/a	chr3:50126883-50126893
11	BRCA1	chr3:50126105-50126680	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:50126039-50127221	GM19193	blood:	n/a	n/a
13	YY1	chr3:50126085-50127168	GM12878	blood:	n/a	chr3:50126369-50126383 chr3:50126949-50126957 chr3:50126901-50126915 chr3:50126945-50126965 chr3:50126948-50126970 chr3:50126375-50126384
14	POLR2A	chr3:50126585-50126888	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:50126022-50127065	Raji	blood:	n/a	n/a
16	YY1	chr3:50126160-50126968	GM12891	blood:	n/a	chr3:50126369-50126383 chr3:50126949-50126957 chr3:50126901-50126915 chr3:50126945-50126965 chr3:50126375-50126384
17	MXI1	chr3:50126128-50126985	HepG2	liver:	n/a	n/a
18	HEY1	chr3:50126129-50127210	K562	blood:	n/a	n/a
19	TAF1	chr3:50126036-50127167	ECC-1	luminal epithelium:	n/a	n/a
20	YY1	chr3:50126031-50127205	H1-hESC	embryonic stem cell:	n/a	chr3:50126369-50126383 chr3:50127190-50127199 chr3:50126949-50126957 chr3:50126901-50126915 chr3:50126945-50126965 chr3:50126948-50126970 chr3:50126375-50126384
21	POLR2A	chr3:50126011-50126630	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:50126063-50127312	GM18505	blood:	n/a	n/a
23	POLR2A	chr3:50125946-50126736	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr3:50126144-50127281	K562	blood:	n/a	n/a
25	POLR2A	chr3:50126051-50126638	K562	blood:	n/a	n/a
26	CHD1	chr3:50126062-50127612	GM12878	blood:	n/a	n/a
27	YY1	chr3:50126125-50126732	A549	lung:	n/a	chr3:50126369-50126383 chr3:50126375-50126384
28	POLR2A	chr3:50126153-50127043	NB4	blood:	n/a	n/a
29	YY1	chr3:50126004-50127181	SK-N-SH_RA	brain:	n/a	chr3:50126369-50126383 chr3:50126949-50126957 chr3:50126901-50126915 chr3:50126945-50126965 chr3:50126948-50126970 chr3:50126375-50126384
30	NFATC1	chr3:50126353-50126709	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:50126107-50126723	HepG2	liver:	n/a	n/a
32	UBTF	chr3:50126084-50127180	K562	blood:	n/a	n/a
33	POLR2A	chr3:50126016-50126660	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr3:50126095-50126865	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:50126031-50127433	GM12892	blood:	n/a	n/a
36	PML	chr3:50125858-50127482	GM12878	blood:	n/a	n/a
37	SIN3AK20	chr3:50126079-50126663	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr3:50126162-50127138	GM12891	blood:	n/a	n/a
39	POLR2A	chr3:50125994-50126645	HCT-116	colon:	n/a	n/a
40	YY1	chr3:50126148-50127078	K562	blood:	n/a	chr3:50126369-50126383 chr3:50126949-50126957 chr3:50126901-50126915 chr3:50126945-50126965 chr3:50126948-50126970 chr3:50126375-50126384
41	TAF1	chr3:50126110-50126613	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr3:50125981-50127176	H1-hESC	embryonic stem cell:	n/a	n/a
43	MYBL2	chr3:50125866-50126622	HepG2	liver:	n/a	n/a
44	MAX	chr3:50126057-50126635	A549	lung:	n/a	n/a
45	MXI1	chr3:50126153-50126690	K562	blood:	n/a	n/a
46	POLR2A	chr3:50126137-50126665	A549	lung:	n/a	n/a
47	POLR2A	chr3:50125949-50126980	HepG2	liver:	n/a	n/a
48	RUNX3	chr3:50125868-50126937	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:50126115-50127115	ECC-1	luminal epithelium:	n/a	n/a
50	STAT5A	chr3:50125866-50127070	GM12878	blood:	n/a	chr3:50126256-50126276

No.	Distal block	Cell Line	Cell type
1	chr3:50125762..50129022-chr3:50137938..50141076,4	K562	blood:
2	chr17:48943215..48944003-chr3:50126322..50126966,2	Hela-S3	cervix:
3	chr3:50126080..50126817-chr3:197025051..197025628,2	Hela-S3	cervix:
4	chr3:50125097..50128236-chr3:50128554..50131975,3	MCF-7	breast:
5	chr1:114447360..114448137-chr3:50126334..50127160,2	NB4	blood:
6	chr3:49966762..49969614-chr3:50125142..50129125,3	K562	blood:
7	chr3:50126575..50128257-chr3:50136862..50139788,2	MCF-7	breast:
8	chr3:49966031..49968659-chr3:50125180..50127794,3	K562	blood:
9	chr3:49975788..49978611-chr3:50125447..50127862,2	MCF-7	breast:
10	chr3:49976300..49979550-chr3:50125389..50128777,3	K562	blood:

Variant related genes	Relation type
RBM5	TF binding region
ENSG00000075711	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000164077	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000227375	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000003756	Chromatin interaction
ENSG00000004534	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12107386	0.87[AFR][1000 genomes]
rs17050905	0.87[AFR][1000 genomes]
rs17050921	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs17050924	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2230592	1.00[YRI][hapmap]
rs56297242	0.81[AFR][1000 genomes]
rs59822920	0.87[AFR][1000 genomes]
rs60065407	0.81[AFR][1000 genomes]
rs73832789	0.81[AFR][1000 genomes]
rs73832800	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv822081	chr3:50120963-50127117	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr3:50125800-50126600	Active TSS	Brain Germinal Matrix	brain
2	chr3:50125800-50126800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr3:50125800-50127400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:50125800-50127600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:50125800-50127600	Active TSS	Brain Substantia Nigra	brain
6	chr3:50125800-50127600	Active TSS	Colonic Mucosa	Colon
7	chr3:50125800-50127600	Active TSS	Colon Smooth Muscle	Colon
8	chr3:50125800-50127600	Active TSS	Esophagus	oesophagus
9	chr3:50125800-50127600	Active TSS	Rectal Smooth Muscle	rectum
10	chr3:50125800-50127600	Active TSS	Osteobl	bone
11	chr3:50125800-50127800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:50125800-50127800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:50125800-50127800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:50125800-50127800	Active TSS	Fetal Brain Female	brain
15	chr3:50125800-50127800	Active TSS	HSMM	muscle
16	chr3:50125800-50128000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:50125800-50128200	Active TSS	Psoas Muscle	Psoas
18	chr3:50126000-50126600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:50126000-50127400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:50126000-50127400	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr3:50126000-50127400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:50126000-50127400	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr3:50126000-50127400	Active TSS	Adipose Nuclei	Adipose
24	chr3:50126000-50127400	Active TSS	Placenta Amnion	Placenta Amnion
25	chr3:50126000-50127400	Active TSS	Thymus	Thymus
26	chr3:50126000-50127400	Bivalent/Poised TSS	HepG2	liver
27	chr3:50126000-50127600	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr3:50126000-50127600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:50126000-50127600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr3:50126000-50127600	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr3:50126000-50127600	Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr3:50126000-50127600	Active TSS	Muscle Satellite Cultured Cells	--
33	chr3:50126000-50127600	Active TSS	Brain Angular Gyrus	brain
34	chr3:50126000-50127600	Active TSS	Brain Cingulate Gyrus	brain
35	chr3:50126000-50127600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr3:50126000-50127600	Active TSS	Fetal Intestine Large	intestine
37	chr3:50126000-50127600	Active TSS	Fetal Intestine Small	intestine
38	chr3:50126000-50127600	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr3:50126000-50127600	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr3:50126000-50127600	Active TSS	Stomach Smooth Muscle	stomach
41	chr3:50126000-50127800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr3:50126000-50127800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:50126000-50127800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr3:50126000-50127800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:50126000-50127800	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr3:50126000-50127800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:50126000-50127800	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr3:50126000-50127800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:50126000-50127800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:50126000-50127800	Active TSS	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links