Variant report

Variant	rs11588450
Chromosome Location	chr1:47000996-47000997
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	CTCF	chr1:47000900-47001050	SK-N-SH_RA	brain:	n/a	chr1:47000945-47000963
2	CTCF	chr1:47000856-47001060	A549	lung:	n/a	chr1:47000945-47000963
3	CTCF	chr1:47000860-47001010	HEK293	kidney:	n/a	chr1:47000945-47000963
4	RAD21	chr1:47000748-47001106	HepG2	liver:	n/a	chr1:47000947-47000961 chr1:47000943-47000962
5	CTCF	chr1:47000860-47001010	BJ	skin:	n/a	chr1:47000945-47000963
6	CTCF	chr1:47000900-47001050	HEEpiC	esophagus:	n/a	chr1:47000945-47000963
7	CTCF	chr1:47000819-47001090	MCF-7	breast:	n/a	chr1:47000945-47000963
8	CTCF	chr1:47000940-47001090	GM12870	blood:	n/a	chr1:47000945-47000963
9	CTCF	chr1:47000900-47001050	HPAF	blood vessel:	n/a	chr1:47000945-47000963
10	CTCF	chr1:47000900-47001050	GM12873	blood:	n/a	chr1:47000945-47000963
11	CTCF	chr1:47000900-47001050	Hela-S3	cervix:	n/a	chr1:47000945-47000963
12	CTCF	chr1:47000823-47001019	A549	lung:	n/a	chr1:47000945-47000963
13	RAD21	chr1:47000697-47001188	HepG2	liver:	n/a	chr1:47000947-47000961 chr1:47000943-47000962
14	CTCF	chr1:47000564-47001240	HCT-116	colon:	n/a	chr1:47000945-47000963
15	CTCF	chr1:47000880-47001030	GM12867	blood:	n/a	chr1:47000945-47000963
16	CTCF	chr1:47000900-47001050	HL-60	blood:	n/a	chr1:47000945-47000963
17	CTCF	chr1:47000880-47001030	GM12873	blood:	n/a	chr1:47000945-47000963
18	CTCF	chr1:47000893-47001008	H1-hESC	embryonic stem cell:	n/a	chr1:47000945-47000963
19	CTCF	chr1:47000900-47001050	HRPEpiC	eye:	n/a	chr1:47000945-47000963
20	CTCF	chr1:47000860-47001010	HMF	breast:	n/a	chr1:47000945-47000963
21	CTCF	chr1:47000860-47001010	SAEC	small airway:	n/a	chr1:47000945-47000963
22	CTCF	chr1:47000618-47001311	SK-N-SH	brain:	n/a	chr1:47000945-47000963
23	CTCF	chr1:47000875-47001050	Kidney_OC	kidney:	n/a	chr1:47000945-47000963
24	CTCF	chr1:47000860-47001010	WERI-Rb-1	eye:	n/a	chr1:47000945-47000963
25	CTCF	chr1:47000817-47001102	NHEK	skin:	n/a	chr1:47000945-47000963
26	CTCF	chr1:47000920-47001070	SAEC	small airway:	n/a	chr1:47000945-47000963
27	CTCF	chr1:47000900-47001050	HVMF	connective:	n/a	chr1:47000945-47000963
28	CTCF	chr1:47000900-47001050	HA-sp	spinal cord:	n/a	chr1:47000945-47000963
29	RAD21	chr1:47000725-47001149	SK-N-SH_RA	brain:	n/a	chr1:47000947-47000961 chr1:47000943-47000962
30	CTCF	chr1:47000880-47001030	GM12875	blood:	n/a	chr1:47000945-47000963
31	MAX	chr1:47000729-47001205	K562	blood:	n/a	n/a
32	CTCF	chr1:47000880-47001030	GM06990	blood:	n/a	chr1:47000945-47000963
33	JUND	chr1:47000765-47001246	HepG2	liver:	n/a	n/a
34	CTCF	chr1:47000900-47001050	HPF	lung:	n/a	chr1:47000945-47000963
35	CTCF	chr1:47000860-47001010	HCM	heart:	n/a	chr1:47000945-47000963
36	CTCF	chr1:47000747-47001178	MCF-7	breast:	n/a	chr1:47000945-47000963
37	RAD21	chr1:47000691-47001148	ECC-1	luminal epithelium:	n/a	chr1:47000947-47000961 chr1:47000943-47000962
38	CTCF	chr1:47000880-47001030	HUVEC	blood vessel:	n/a	chr1:47000945-47000963
39	ZNF384	chr1:47000804-47001105	K562	blood:	n/a	n/a
40	MAX	chr1:47000840-47001067	K562	blood:	n/a	n/a
41	RAD21	chr1:47000779-47001196	MCF-7	breast:	n/a	chr1:47000947-47000961 chr1:47000943-47000962
42	CTCF	chr1:47000900-47001050	WI-38	lung:	n/a	chr1:47000945-47000963
43	RAD21	chr1:47000641-47001217	HCT-116	colon:	n/a	chr1:47000947-47000961 chr1:47000943-47000962
44	CTCF	chr1:47000860-47001084	T-47D	breast:	n/a	chr1:47000945-47000963
45	RAD21	chr1:47000867-47001070	SK-N-SH_RA	brain:	n/a	chr1:47000947-47000961 chr1:47000943-47000962
46	CTCF	chr1:47000860-47001010	GM12864	blood:	n/a	chr1:47000945-47000963
47	CTCF	chr1:47000860-47001010	AG04449	skin:	n/a	chr1:47000945-47000963
48	CTCF	chr1:47000860-47001010	AoAF	blood vessel:	n/a	chr1:47000945-47000963
49	CTCF	chr1:47000920-47001070	BE2_C	brain:	n/a	chr1:47000945-47000963
50	CTCF	chr1:47000833-47001093	MCF-7	breast:	n/a	chr1:47000945-47000963

No.	Distal block	Cell Line	Cell type
1	chr1:46995357..46997930-chr1:46998172..47001101,2	K562	blood:
2	chr1:46872033..46872647-chr1:47000499..47001417,2	K562	blood:
3	chr1:46870622..46873242-chr1:47000885..47003124,2	K562	blood:
4	chr1:46942860..46943709-chr1:47000567..47001413,4	MCF-7	breast:
5	chr1:46999703..47001765-chr1:47004931..47007448,2	K562	blood:
6	chr1:46912286..46913258-chr1:47000199..47001465,3	K562	blood:
7	chr1:46942855..46943565-chr1:47000606..47001211,2	K562	blood:
8	chr1:46991343..46993867-chr1:46999372..47001574,2	K562	blood:
9	chr1:46995449..46997636-chr1:47000610..47003037,2	K562	blood:
10	chr1:47000463..47001603-chr1:47013528..47014314,3	K562	blood:
11	chr1:46912494..46913218-chr1:47000111..47001290,4	MCF-7	breast:

Variant related genes	Relation type
MKNK1-AS1	TF binding region
ENSG00000117480	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1267301	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs1267302	0.81[CEU][hapmap];0.88[YRI][hapmap];0.89[EUR][1000 genomes]
rs1267304	0.85[EUR][1000 genomes]
rs1267308	0.80[EUR][1000 genomes]
rs1267309	0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs1267310	0.80[EUR][1000 genomes]
rs1267312	0.81[EUR][1000 genomes]
rs1267313	0.81[EUR][1000 genomes]
rs1745370	0.80[EUR][1000 genomes]
rs1745371	0.81[EUR][1000 genomes]
rs2404611	0.99[EUR][1000 genomes]
rs2476162	0.90[EUR][1000 genomes]
rs2476164	0.81[EUR][1000 genomes]
rs2486163	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3737740	0.99[EUR][1000 genomes]
rs57100184	0.98[EUR][1000 genomes]
rs59935547	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61395024	0.92[EUR][1000 genomes]
rs61783087	0.99[EUR][1000 genomes]
rs6670699	0.99[EUR][1000 genomes]
rs6696219	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703148	0.81[EUR][1000 genomes]
rs72894667	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519040	0.81[EUR][1000 genomes]
rs7524253	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7542296	0.99[EUR][1000 genomes]
rs942255	0.85[YRI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv998422	chr1:46969626-47023671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv534953	chr1:46969626-47023671	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1010578	chr1:46977818-47010579	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11588450	MKNK1	cis	cerebellum	SCAN
rs11588450	CLDN19	cis	cerebellum	SCAN
rs11588450	SLC2A1	cis	parietal	SCAN
rs11588450	KDM4A	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46999600-47035000	Weak transcription	Right Atrium	heart
2	chr1:46999800-47001000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:46999800-47001000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:46999800-47001000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:46999800-47007600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:47000000-47002800	Weak transcription	Spleen	Spleen
7	chr1:47000200-47001000	Weak transcription	Hela-S3	cervix
8	chr1:47000800-47002600	Enhancers	K562	blood

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