Variant report

Variant	rs7946133
Chromosome Location	chr11:17791822-17791823
allele	G/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	chr11:17791700-17791850	GM12866	blood:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
2	CTCF	chr11:17791720-17791870	RPTEC	kidney:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
3	RXRA	chr11:17791578-17791857	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr11:17791653-17791864	K562	blood:	n/a	n/a
5	CTCF	chr11:17791581-17791867	H1-hESC	embryonic stem cell:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
6	CTCF	chr11:17791680-17791830	SK-N-SH_RA	brain:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
7	SIN3AK20	chr11:17791402-17792166	MCF-7	breast:	n/a	n/a
8	CTCF	chr11:17791700-17791850	GM12868	blood:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
9	CEBPD	chr11:17791540-17791900	HepG2	liver:	n/a	n/a
10	FOXA1	chr11:17791611-17791894	ECC-1	luminal epithelium:	n/a	chr11:17791699-17791714 chr11:17791741-17791756
11	ESR1	chr11:17791549-17791873	ECC-1	luminal epithelium:	n/a	n/a
12	CTCF	chr11:17791680-17791830	Hela-S3	cervix:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
13	YY1	chr11:17791552-17791924	HepG2	liver:	n/a	n/a
14	CTCF	chr11:17791617-17791831	MCF-7	breast:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
15	CTCF	chr11:17791720-17791870	GM12874	blood:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
16	RCOR1	chr11:17791571-17791892	K562	blood:	n/a	n/a
17	CTCF	chr11:17791700-17791850	HCT-116	colon:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
18	MYC	chr11:17791564-17791892	HepG2	liver:	n/a	n/a
19	FOXA1	chr11:17791559-17791835	T-47D	breast:	n/a	chr11:17791699-17791714 chr11:17791741-17791756
20	NR2F2	chr11:17791363-17792134	MCF-7	breast:	n/a	n/a
21	RCOR1	chr11:17791448-17791938	HepG2	liver:	n/a	n/a
22	CTCF	chr11:17791700-17791850	HFF-Myc	foreskin:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
23	NR2F2	chr11:17791459-17791988	K562	blood:	n/a	n/a
24	CTCF	chr11:17791700-17791850	HAc	cerebellar:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
25	MAX	chr11:17791323-17792082	HepG2	liver:	n/a	n/a
26	ESR1	chr11:17791634-17791905	ECC-1	luminal epithelium:	n/a	n/a
27	CTCF	chr11:17791624-17791843	H1-hESC	embryonic stem cell:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
28	CTCF	chr11:17791680-17791830	GM12867	blood:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
29	CTCF	chr11:17791559-17791836	K562	blood:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
30	CEBPB	chr11:17791598-17791899	HepG2	liver:	n/a	n/a
31	CTCF	chr11:17791800-17791950	A549	lung:	n/a	n/a
32	CTCF	chr11:17791608-17791829	GM12892	blood:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
33	GTF2F1	chr11:17791740-17791890	K562	blood:	n/a	n/a
34	MAFK	chr11:17791695-17791936	HepG2	liver:	n/a	n/a
35	CTCF	chr11:17791559-17791861	HepG2	liver:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
36	YY1	chr11:17791549-17791983	HepG2	liver:	n/a	n/a
37	ZNF143	chr11:17791676-17791865	Hela-S3	cervix:	n/a	n/a
38	RAD21	chr11:17791523-17791852	HepG2	liver:	n/a	chr11:17791734-17791747
39	ZNF143	chr11:17791590-17791836	K562	blood:	n/a	n/a
40	CTCF	chr11:17791680-17791830	HRPEpiC	eye:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
41	RAD21	chr11:17791561-17791931	H1-hESC	embryonic stem cell:	n/a	chr11:17791734-17791747
42	FOXA1	chr11:17791606-17791849	T-47D	breast:	n/a	chr11:17791699-17791714 chr11:17791741-17791756
43	MYC	chr11:17791580-17791882	K562	blood:	n/a	n/a
44	SP1	chr11:17791520-17792026	HepG2	liver:	n/a	chr11:17791687-17791696 chr11:17791686-17791698 chr11:17791688-17791697 chr11:17791686-17791698 chr11:17791687-17791697 chr11:17791683-17791697 chr11:17791879-17791893
45	MYBL2	chr11:17791379-17792015	HepG2	liver:	n/a	n/a
46	MYBL2	chr11:17791291-17792013	HepG2	liver:	n/a	n/a
47	MAX	chr11:17791646-17791908	K562	blood:	n/a	n/a
48	CTCF	chr11:17791531-17791873	K562	blood:	n/a	chr11:17791735-17791748 chr11:17791733-17791751
49	MAZ	chr11:17791525-17791904	HepG2	liver:	n/a	n/a
50	ARID3A	chr11:17791527-17791963	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:17791261..17792211-chr11:17946174..17946920,4	MCF-7	breast:
2	chr11:17789104..17793559-chr11:17796092..17800270,5	MCF-7	breast:
3	chr11:17791157..17792211-chr11:17946174..17946920,6	MCF-7	breast:
4	chr11:17790395..17791963-chr11:17795616..17797848,2	K562	blood:
5	chr11:17791247..17794224-chr11:17800123..17802336,2	MCF-7	breast:
6	chr11:17791549..17792453-chr11:17833752..17834540,3	MCF-7	breast:
7	chr11:17783850..17786298-chr11:17789626..17792965,4	K562	blood:
8	chr11:17791307..17792105-chr11:17946399..17946914,2	MCF-7	breast:
9	chr11:17791223..17792205-chr11:17834136..17835260,3	MCF-7	breast:
10	chr11:17426978..17427915-chr11:17791365..17792221,7	MCF-7	breast:
11	chr11:17426978..17427915-chr11:17791365..17792205,5	MCF-7	breast:

Variant related genes	Relation type
KCNC1	TF binding region
ENSG00000129159	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10741733	0.81[ASN][1000 genomes]
rs10766427	0.82[ASN][1000 genomes]
rs10766428	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10766430	0.82[ASN][1000 genomes]
rs10832856	0.82[ASN][1000 genomes]
rs10832857	0.82[ASN][1000 genomes]
rs11602509	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1989452	0.82[ASN][1000 genomes]
rs2107580	0.86[JPT][hapmap]
rs2299635	0.81[ASN][1000 genomes]
rs2299636	0.82[ASN][1000 genomes]
rs2299637	0.82[ASN][1000 genomes]
rs3781949	0.88[AMR][1000 genomes]
rs6486397	0.82[ASN][1000 genomes]
rs72632993	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467717	chr11:17713507-17791822	Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv553588	chr11:17713507-17791822	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1038119	chr11:17744915-17794577	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv467718	chr11:17744992-17809724	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv553589	chr11:17744992-17809724	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv516767	chr11:17758587-17809724	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv832078	chr11:17780503-17953521	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv1043973	chr11:17781560-17869896	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7946133	SAAL1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17773400-17795600	Weak transcription	Brain Hippocampus Middle	brain
2	chr11:17787800-17796000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:17787800-17801400	Weak transcription	Brain Angular Gyrus	brain
4	chr11:17788000-17795800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:17788000-17811400	Weak transcription	Brain Anterior Caudate	brain
6	chr11:17788200-17793000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:17788200-17793000	Weak transcription	Brain Germinal Matrix	brain
8	chr11:17788200-17793400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:17788400-17802000	Weak transcription	Fetal Brain Male	brain
10	chr11:17790200-17792600	Weak transcription	Fetal Brain Female	brain
11	chr11:17791200-17792000	Enhancers	Right Atrium	heart
12	chr11:17791200-17792600	Enhancers	Liver	Liver
13	chr11:17791400-17792000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr11:17791400-17792000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:17791400-17792000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr11:17791400-17792000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr11:17791400-17792200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr11:17791400-17792400	Flanking Active TSS	HepG2	liver
19	chr11:17791400-17792600	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr11:17791400-17792800	Enhancers	Stomach Mucosa	stomach
21	chr11:17791400-17793000	Enhancers	Duodenum Mucosa	Duodenum
22	chr11:17791400-17793200	Enhancers	Fetal Intestine Small	intestine
23	chr11:17791400-17793200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr11:17791600-17792000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr11:17791600-17792000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:17791600-17792000	Enhancers	Gastric	stomach
27	chr11:17791600-17792000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr11:17791600-17792000	Enhancers	A549	lung
29	chr11:17791600-17792400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:17791600-17792400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:17791600-17792400	Enhancers	Pancreas	Pancrea
32	chr11:17791600-17792400	Enhancers	Hela-S3	cervix
33	chr11:17791600-17793200	Enhancers	Fetal Intestine Large	intestine
34	chr11:17791800-17792000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:17791800-17792400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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