Variant report

Variant	rs503250
Chromosome Location	chr11:66372066-66372067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66366106..66376502-chr11:66378243..66386807,17	K562	blood:
2	chr11:66369958..66372351-chr11:66375858..66377391,2	K562	blood:
3	chr11:66371248..66380060-chr11:66381222..66386481,17	MCF-7	breast:
4	chr11:66362395..66364354-chr11:66370212..66372742,2	MCF-7	breast:
5	chr11:66365616..66367263-chr11:66370515..66372888,2	K562	blood:

Variant related genes	Relation type
ENSG00000239306	Chromatin interaction
ENSG00000199325	Chromatin interaction
ENSG00000248643	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs12577111	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes]
rs12804382	0.80[EUR][1000 genomes]
rs12805133	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs1671062	0.82[JPT][hapmap]
rs1671064	0.83[CHB][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs1791684	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1815739	0.83[CHB][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]
rs2000939	0.80[ASN][1000 genomes]
rs2276138	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2279863	0.80[JPT][hapmap]
rs3018318	0.81[ASN][1000 genomes]
rs34900764	0.89[EUR][1000 genomes]
rs3741363	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs474602	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs477557	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs486584	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4930387	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs498045	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs508443	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs509556	0.83[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs535211	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs540874	0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.81[ASN][1000 genomes]
rs545009	0.81[ASN][1000 genomes]
rs556759	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560556	0.83[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs566673	0.81[CEU][hapmap]
rs569818	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs572846	0.83[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs577023	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs577335	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs580910	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs608248	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs615205	0.80[ASN][1000 genomes]
rs618838	0.81[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs636128	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs677488	0.83[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs678397	0.83[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs692892	0.96[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs8432	0.82[JPT][hapmap];0.88[MKK][hapmap];0.80[YRI][hapmap]

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	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs503250	CCDC85B	cis	parietal	SCAN
rs503250	CCS	cis	lymphoblastoid	seeQTL
rs503250	BBS1	cis	cerebellum	SCAN
rs503250	CDC42EP2	cis	cerebellum	SCAN
rs503250	CTSF	cis	parietal	SCAN
rs503250	YIF1A	cis	cerebellum	SCAN
rs503250	KDM2A	cis	cerebellum	SCAN
rs503250	ACTN3	cis	Muscle Skeletal	GTEx
rs503250	CTSF	cis	cerebellum	SCAN
rs503250	PRDX5	cis	cerebellum	SCAN
rs503250	CCS	cis	multi-tissue	Pritchard
rs503250	TRMT112	cis	cerebellum	SCAN
rs503250	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs503250	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs503250	ACTN3	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66361400-66382800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:66361400-66383400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:66361600-66372800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr11:66361600-66374400	Weak transcription	Psoas Muscle	Psoas
5	chr11:66361600-66377000	Weak transcription	HUVEC	blood vessel
6	chr11:66362200-66377200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:66363000-66372400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:66363000-66377200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:66363200-66383200	Weak transcription	Fetal Kidney	kidney
10	chr11:66363400-66382800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr11:66363400-66383200	Weak transcription	Fetal Brain Male	brain
12	chr11:66363600-66374600	Weak transcription	Stomach Mucosa	stomach
13	chr11:66363600-66377200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:66363800-66377400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr11:66366000-66374200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:66366400-66373800	Strong transcription	Brain Anterior Caudate	brain
17	chr11:66366400-66374400	Strong transcription	Placenta	Placenta
18	chr11:66366400-66374600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:66366400-66374600	Strong transcription	Fetal Intestine Small	intestine
20	chr11:66366400-66375000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:66366400-66375200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:66366400-66375200	Strong transcription	Primary T cells from cord blood	blood
23	chr11:66366400-66375200	Strong transcription	Fetal Thymus	thymus
24	chr11:66366400-66375600	Strong transcription	Thymus	Thymus
25	chr11:66366400-66376000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:66366600-66373600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr11:66366600-66373600	Strong transcription	Fetal Lung	lung
28	chr11:66366600-66374000	Strong transcription	Fetal Intestine Large	intestine
29	chr11:66367400-66372200	Weak transcription	Hela-S3	cervix
30	chr11:66367400-66383400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:66367600-66372400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr11:66368000-66372400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:66368000-66372800	Weak transcription	Pancreas	Pancrea
34	chr11:66368200-66372800	Weak transcription	Small Intestine	intestine
35	chr11:66368600-66375200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:66369000-66374600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr11:66369400-66373600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:66369400-66373800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr11:66369400-66374800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:66369600-66373800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr11:66369800-66373800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr11:66369800-66373800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr11:66369800-66374000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr11:66369800-66375000	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr11:66370000-66373800	Strong transcription	Rectal Smooth Muscle	rectum
46	chr11:66370000-66374200	Strong transcription	Colon Smooth Muscle	Colon
47	chr11:66370000-66374400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr11:66370200-66374400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:66370400-66372600	Weak transcription	Esophagus	oesophagus
50	chr11:66370400-66372800	Weak transcription	Left Ventricle	heart

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