Variant report

Variant	rs4968469
Chromosome Location	chr17:60137085-60137086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60131533..60136089-chr17:60136212..60137998,4	MCF-7	breast:
2	chr17:60108114..60110987-chr17:60135242..60137203,2	K562	blood:
3	chr17:60020965..60024852-chr17:60134621..60138471,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11079461	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11079464	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs11649711	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11870331	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12450995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2048718	0.81[CHD][hapmap]
rs28610444	0.85[AMR][1000 genomes]
rs28755966	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4456566	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4479315	0.88[ASN][1000 genomes]
rs4493126	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968410	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4968466	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4968473	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968477	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs58046762	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6504079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67274807	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs686994	0.83[JPT][hapmap]
rs7207930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7210061	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7218545	0.84[EUR][1000 genomes]
rs7222262	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72845411	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72845416	0.84[EUR][1000 genomes]
rs72845417	0.84[EUR][1000 genomes]
rs72845418	0.84[EUR][1000 genomes]
rs8067092	0.81[CHD][hapmap]
rs8072101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8081599	0.82[EUR][1000 genomes]
rs8081805	0.85[EUR][1000 genomes]
rs8081812	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9303455	0.85[EUR][1000 genomes]
rs9747976	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9889324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9889676	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs9902812	0.94[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap]
rs9908352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9913443	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062816	chr17:60074670-60470465	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	esv2753884	chr17:60077852-60190630	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv2755037	chr17:60086508-60386211	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3415630	chr17:60124819-60401635	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4968469	MED13	cis	cerebellum	SCAN
rs4968469	MRPS23	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr17:60099400-60139000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:60108000-60141400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:60108800-60139000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:60109000-60141200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:60110600-60139800	Weak transcription	Spleen	Spleen
7	chr17:60111200-60140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:60111400-60138400	Weak transcription	Fetal Brain Male	brain
9	chr17:60111400-60140400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:60111400-60141400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr17:60115000-60140000	Weak transcription	Gastric	stomach
12	chr17:60116000-60139800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:60116200-60139800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr17:60116600-60139000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr17:60117400-60139200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr17:60124200-60139200	Weak transcription	Right Ventricle	heart
17	chr17:60126200-60141600	Weak transcription	Esophagus	oesophagus
18	chr17:60129600-60139000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr17:60129800-60139000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr17:60129800-60139000	Weak transcription	Fetal Kidney	kidney
21	chr17:60130000-60139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr17:60130600-60139200	Weak transcription	HUVEC	blood vessel
23	chr17:60131200-60138000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr17:60132400-60138800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:60133200-60137600	Weak transcription	Lung	lung
26	chr17:60133400-60137800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr17:60133600-60140200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr17:60133800-60137200	Enhancers	Colon Smooth Muscle	Colon
29	chr17:60133800-60137200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
30	chr17:60133800-60140000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr17:60133800-60140000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr17:60134000-60140000	Weak transcription	Small Intestine	intestine
33	chr17:60134200-60137600	Weak transcription	Left Ventricle	heart
34	chr17:60134200-60139600	Genic enhancers	HepG2	liver
35	chr17:60134200-60141000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr17:60134600-60140800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
37	chr17:60134800-60137800	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr17:60134800-60139200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr17:60134800-60140000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr17:60135200-60139000	Weak transcription	NHLF	lung
41	chr17:60135200-60139600	Weak transcription	Stomach Mucosa	stomach
42	chr17:60135200-60139800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr17:60135400-60139200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr17:60135400-60139200	Weak transcription	Adipose Nuclei	Adipose
45	chr17:60135600-60138400	Weak transcription	Fetal Brain Female	brain
46	chr17:60135600-60139200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr17:60135600-60140000	Weak transcription	HSMMtube	muscle
48	chr17:60135800-60139200	Strong transcription	HSMM	muscle
49	chr17:60135800-60139800	Weak transcription	Aorta	Aorta
50	chr17:60136000-60137200	Strong transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links