Variant report

Variant	rs1516617
Chromosome Location	chr11:83527607-83527608
allele	A/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	chr11:83526446-83527996	SK-N-MC	brain:	n/a	n/a
2	CTCF	chr11:83527475-83528128	HCT-116	colon:	n/a	chr11:83527816-83527832 chr11:83527815-83527833 chr11:83527810-83527831 chr11:83527820-83527828
3	RFX5	chr11:83527456-83527969	Hela-S3	cervix:	n/a	n/a
4	RAD21	chr11:83527574-83528001	SK-N-SH_RA	brain:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
5	CTCF	chr11:83526550-83528109	SK-N-SH	brain:	n/a	chr11:83527816-83527832 chr11:83527815-83527833 chr11:83527810-83527831 chr11:83527820-83527828
6	CTCF	chr11:83527594-83528030	A549	lung:	n/a	chr11:83527816-83527832 chr11:83527815-83527833 chr11:83527810-83527831 chr11:83527820-83527828
7	RAD21	chr11:83527441-83528109	MCF-7	breast:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
8	RAD21	chr11:83527561-83528097	A549	lung:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
9	RAD21	chr11:83527602-83528102	MCF-7	breast:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
10	FOXA1	chr11:83527501-83527888	T-47D	breast:	n/a	n/a
11	RAD21	chr11:83527592-83527984	GM12878	blood:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
12	RAD21	chr11:83527570-83528052	H1-hESC	embryonic stem cell:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
13	RAD21	chr11:83527512-83528039	HepG2	liver:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
14	RAD21	chr11:83527505-83528092	A549	lung:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
15	RAD21	chr11:83527571-83527949	ECC-1	luminal epithelium:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
16	GATA3	chr11:83527410-83528043	T-47D	breast:	n/a	n/a
17	CTCF	chr11:83527603-83527992	HepG2	liver:	n/a	chr11:83527816-83527832 chr11:83527815-83527833 chr11:83527810-83527831 chr11:83527820-83527828
18	RAD21	chr11:83527511-83527972	HCT-116	colon:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
19	CTCF	chr11:83527560-83527710	HFF-Myc	foreskin:	n/a	n/a
20	RAD21	chr11:83526898-83528074	Hela-S3	cervix:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
21	CTCF	chr11:83527592-83528104	IMR90	lung:	n/a	chr11:83527816-83527832 chr11:83527815-83527833 chr11:83527810-83527831 chr11:83527820-83527828
22	EP300	chr11:83527383-83528008	T-47D	breast:	n/a	n/a
23	CTCF	chr11:83527537-83528022	MCF-7	breast:	n/a	chr11:83527816-83527832 chr11:83527815-83527833 chr11:83527810-83527831 chr11:83527820-83527828
24	RAD21	chr11:83527100-83528262	SK-N-SH	brain:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
25	RAD21	chr11:83527464-83528039	HCT-116	colon:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
26	RAD21	chr11:83527579-83528047	IMR90	lung:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
27	RAD21	chr11:83527559-83528034	H1-hESC	embryonic stem cell:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
28	CTCF	chr11:83527454-83528240	A549	lung:	n/a	chr11:83527816-83527832 chr11:83527815-83527833 chr11:83527810-83527831 chr11:83527820-83527828
29	GATA3	chr11:83527432-83527988	T-47D	breast:	n/a	n/a
30	SMC3	chr11:83526469-83528039	Hela-S3	cervix:	n/a	chr11:83527817-83527831
31	SMC3	chr11:83527026-83528274	SK-N-SH	brain:	n/a	chr11:83527817-83527831
32	RAD21	chr11:83527562-83528025	H1-hESC	embryonic stem cell:	n/a	chr11:83527823-83527830 chr11:83527819-83527828 chr11:83527813-83527832
33	CTCF	chr11:83527580-83527730	HAc	cerebellar:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:83527114..83529633-chr11:83531470..83533535,2	K562	blood:
2	chr11:83003679..83004499-chr11:83527362..83528093,2	MCF-7	breast:
3	chr11:83512525..83513084-chr11:83527310..83527841,2	MCF-7	breast:
4	chr11:83232530..83233170-chr11:83527353..83527936,3	MCF-7	breast:
5	chr11:83434924..83435893-chr11:83527425..83528252,2	MCF-7	breast:
6	chr11:83003693..83004630-chr11:83527479..83528129,2	MCF-7	breast:
7	chr11:83232403..83232986-chr11:83527322..83527852,2	MCF-7	breast:

Variant related genes	Relation type
LDHAL6DP	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10792693	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1113082	0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11233755	0.88[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1155448	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11820522	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1226063	1.00[YRI][hapmap]
rs12794931	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12799838	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1400310	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1451391	0.81[EUR][1000 genomes]
rs1451392	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1451393	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1516618	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][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]
rs1516622	0.91[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1516623	0.83[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1516624	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1961555	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2040310	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2040311	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2040312	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851171	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3862775	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3862776	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4117186	0.87[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4362168	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4396309	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4480568	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6592143	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6592144	0.96[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6592145	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6592147	1.00[YRI][hapmap]
rs6592148	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7107629	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7122007	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7124506	0.92[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7130803	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs715858	1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7483854	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7937553	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7937829	0.84[EUR][1000 genomes]
rs7941665	0.87[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7946278	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7946494	0.87[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7947211	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9888248	1.00[YRI][hapmap]

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:83523800-83527800	Enhancers	Brain Hippocampus Middle	brain
2	chr11:83525600-83527800	Enhancers	Brain Cingulate Gyrus	brain
3	chr11:83525800-83527800	Enhancers	Brain Angular Gyrus	brain
4	chr11:83525800-83527800	Enhancers	Brain Anterior Caudate	brain
5	chr11:83526000-83530200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:83526200-83527800	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr11:83526200-83528000	Enhancers	Hela-S3	cervix
8	chr11:83526800-83534600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:83527000-83529400	Weak transcription	HMEC	breast
10	chr11:83527200-83531200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:83527400-83529200	Weak transcription	HUVEC	blood vessel
12	chr11:83527400-83529200	Weak transcription	NH-A	brain
13	chr11:83527600-83529200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:83527600-83530600	Weak transcription	Brain Substantia Nigra	brain
15	chr11:83527600-83532600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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