Variant report

Variant	rs12146493
Chromosome Location	chr11:65547333-65547334
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	ELF1	chr11:65547328-65547786	K562	blood:	n/a	n/a
2	TCF12	chr11:65547145-65548096	A549	lung:	n/a	chr11:65547435-65547445 chr11:65547798-65547808 chr11:65547237-65547244
3	EP300	chr11:65547318-65547809	H1-hESC	embryonic stem cell:	n/a	chr11:65547639-65547648
4	POLR2A	chr11:65547002-65548816	K562	blood:	n/a	n/a
5	CEBPB	chr11:65547231-65547480	K562	blood:	n/a	n/a
6	CTCF	chr11:65546574-65548185	HCT-116	colon:	n/a	chr11:65547604-65547622 chr11:65546607-65546620 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
7	CTCF	chr11:65547290-65547842	K562	blood:	n/a	chr11:65547604-65547622 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
8	CTCF	chr11:65547323-65547840	IMR90	lung:	n/a	chr11:65547604-65547622 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
9	REST	chr11:65547264-65547794	PFSK-1	brain:	n/a	chr11:65547417-65547426 chr11:65547469-65547479
10	CTCF	chr11:65547318-65547843	HepG2	liver:	n/a	chr11:65547604-65547622 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
11	GABPA	chr11:65547276-65547924	K562	blood:	n/a	chr11:65547639-65547648
12	CEBPB	chr11:65547152-65547623	A549	lung:	n/a	n/a
13	BCL3	chr11:65547281-65548124	A549	lung:	n/a	chr11:65547639-65547652 chr11:65547933-65547942 chr11:65547530-65547538 chr11:65548101-65548114 chr11:65547570-65547583 chr11:65547443-65547456
14	CTCF	chr11:65547303-65547830	GM12878	blood:	n/a	chr11:65547604-65547622 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
15	MAX	chr11:65547294-65548806	A549	lung:	n/a	chr11:65547898-65547907 chr11:65548277-65548287
16	CEBPB	chr11:65547211-65547571	HepG2	liver:	n/a	n/a
17	CTCF	chr11:65547221-65547346	Gliobla	brain:	n/a	n/a
18	MAX	chr11:65547309-65547987	H1-hESC	embryonic stem cell:	n/a	chr11:65547898-65547907
19	FOXP2	chr11:65547253-65547823	PFSK-1	brain:	n/a	n/a
20	RAD21	chr11:65547317-65547931	MCF-7	breast:	n/a	chr11:65547520-65547539 chr11:65547605-65547624 chr11:65547393-65547407
21	CEBPB	chr11:65547072-65547738	MCF-7	breast:	n/a	n/a
22	REST	chr11:65547294-65547626	H1-hESC	embryonic stem cell:	n/a	chr11:65547417-65547426 chr11:65547469-65547479
23	JUN	chr11:65547162-65548695	K562	blood:	n/a	chr11:65548558-65548568 chr11:65548399-65548410 chr11:65547640-65547649 chr11:65548557-65548569
24	ATF2	chr11:65547319-65547809	H1-hESC	embryonic stem cell:	n/a	n/a
25	YY1	chr11:65547279-65547815	K562	blood:	n/a	chr11:65547637-65547651 chr11:65547698-65547707 chr11:65547643-65547652 chr11:65547631-65547645
26	TAF1	chr11:65547330-65547939	A549	lung:	n/a	n/a
27	CEBPB	chr11:65547211-65547575	IMR90	lung:	n/a	n/a
28	POLR2A	chr11:65547144-65547860	K562	blood:	n/a	n/a
29	CBX3	chr11:65547325-65547847	K562	blood:	n/a	n/a
30	CTCF	chr11:65547094-65549149	SK-N-SH	brain:	n/a	chr11:65547604-65547622 chr11:65548861-65548874 chr11:65548520-65548533 chr11:65548865-65548874 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65548602-65548615 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
31	HEY1	chr11:65547252-65548458	K562	blood:	n/a	chr11:65548169-65548184 chr11:65548384-65548399 chr11:65547463-65547478 chr11:65547629-65547644 chr11:65547636-65547651 chr11:65548181-65548196
32	CEBPB	chr11:65547295-65547503	HepG2	liver:	n/a	n/a
33	SRF	chr11:65547289-65547798	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr11:65547251-65547922	A549	lung:	n/a	chr11:65547604-65547622 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
35	CTCF	chr11:65547200-65547350	GM12865	blood:	n/a	n/a
36	RAD21	chr11:65547246-65547855	A549	lung:	n/a	chr11:65547520-65547539 chr11:65547605-65547624 chr11:65547393-65547407
37	RAD21	chr11:65547140-65548075	HCT-116	colon:	n/a	chr11:65547520-65547539 chr11:65547605-65547624 chr11:65547393-65547407
38	CEBPB	chr11:65547196-65547650	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr11:65547164-65547954	GM19240	blood:	n/a	chr11:65547604-65547622 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
40	ATF2	chr11:65547304-65547708	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr11:65547164-65547956	MCF-7	breast:	n/a	chr11:65547604-65547622 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
42	YY1	chr11:65547296-65548021	GM12892	blood:	n/a	chr11:65547637-65547651 chr11:65547698-65547707 chr11:65547643-65547652 chr11:65547631-65547645
43	FOXM1	chr11:65547182-65547928	GM12878	blood:	n/a	n/a
44	TCF12	chr11:65547217-65548169	ECC-1	luminal epithelium:	n/a	chr11:65547435-65547445 chr11:65547798-65547808 chr11:65547237-65547244
45	ELF1	chr11:65547277-65548688	GM12878	blood:	n/a	n/a
46	CTCF	chr11:65547098-65547990	GM12892	blood:	n/a	chr11:65547604-65547622 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
47	POLR2A	chr11:65547322-65548762	GM12878	blood:	n/a	n/a
48	CTCF	chr11:65546888-65549134	A549	lung:	n/a	chr11:65547604-65547622 chr11:65548861-65548874 chr11:65548520-65548533 chr11:65548865-65548874 chr11:65547607-65547620 chr11:65547727-65547740 chr11:65548602-65548615 chr11:65547605-65547621 chr11:65547607-65547620 chr11:65547519-65547537
49	SP4	chr11:65547300-65547797	H1-hESC	embryonic stem cell:	n/a	chr11:65547540-65547551
50	TAF7	chr11:65547310-65547766	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64949318..64950980-chr11:65546666..65549109,2	MCF-7	breast:
2	chr11:65547331..65547857-chr11:65584018..65584938,2	MCF-7	breast:
3	chr11:65477911..65483635-chr11:65545629..65549670,11	K562	blood:
4	chr11:65546923..65549109-chr11:65560977..65565317,4	K562	blood:
5	chr11:65544951..65562337-chr11:65623093..65630859,34	MCF-7	breast:
6	chr11:65546164..65550034-chr11:65665205..65668429,3	MCF-7	breast:
7	chr11:65545624..65552162-chr11:65622017..65629334,15	K562	blood:
8	chr11:65545480..65548295-chr11:65624014..65629369,5	MCF-7	breast:
9	chr11:65546714..65547677-chr11:65557876..65558611,3	MCF-7	breast:
10	chr11:65545987..65548666-chr11:65554230..65557097,2	K562	blood:
11	chr11:65547324..65548019-chr11:65655670..65656173,2	K562	blood:
12	chr11:65544303..65548645-chr11:65657766..65659706,5	K562	blood:
13	chr11:65478312..65481456-chr11:65546233..65549223,4	MCF-7	breast:
14	chr11:65478523..65481403-chr11:65546217..65549249,4	K562	blood:
15	chr11:65481897..65483713-chr11:65546531..65549436,2	K562	blood:
16	chr11:65547235..65549033-chr11:65639667..65642031,2	K562	blood:
17	chr11:65545624..65551607-chr11:65624049..65629334,14	K562	blood:
18	chr11:65546756..65549287-chr11:65665395..65667925,3	K562	blood:
19	chr11:65546319..65548897-chr11:65656816..65659739,4	K562	blood:
20	chr11:65487099..65491310-chr11:65543476..65547938,6	MCF-7	breast:
21	chr11:65484089..65489642-chr11:65545405..65550834,8	K562	blood:
22	chr11:65546347..65549308-chr11:65631911..65633845,2	MCF-7	breast:
23	chr11:65546195..65548031-chr11:65766372..65768235,2	K562	blood:
24	chr11:65484089..65489445-chr11:65545173..65550834,9	K562	blood:
25	chr11:65546169..65552016-chr11:65555022..65558350,9	K562	blood:
26	chr11:65546756..65549287-chr11:65665686..65670324,5	K562	blood:

Variant related genes	Relation type
ENSG00000175827	TF binding region
ENSG00000172922	Chromatin interaction
ENSG00000172818	Chromatin interaction
ENSG00000175592	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000255404	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000255120	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000172638	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10896041	0.84[ASN][1000 genomes]
rs1193496	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs12293022	0.87[ASN][1000 genomes]
rs12801731	0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[ASN][1000 genomes]
rs2508301	0.90[ASN][1000 genomes]
rs2508303	0.90[ASN][1000 genomes]
rs495961	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs498354	0.87[ASN][1000 genomes]
rs502468	0.86[ASN][1000 genomes]
rs522800	0.89[ASN][1000 genomes]
rs546202	0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[LWK][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs570954	0.82[CHB][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs574483	0.87[ASN][1000 genomes]
rs603326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs603645	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs610037	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[ASN][1000 genomes]
rs614771	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs61895666	0.87[ASN][1000 genomes]
rs61895677	0.88[ASN][1000 genomes]
rs669742	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
4	nsv897758	chr11:65490756-65564035	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv897759	chr11:65543827-65554502	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv897760	chr11:65545306-65559266	Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12146493	SF3B2	cis	cerebellum	SCAN
rs12146493	ALDH3B1	cis	cerebellum	SCAN
rs12146493	SNX32	cis	parietal	SCAN
rs12146493	FTH1	cis	parietal	SCAN
rs12146493	DKFZp761E198	cis	multi-tissue	Pritchard
rs12146493	NXF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65544200-65547600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:65545400-65547400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:65545600-65547600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:65545800-65547400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:65546400-65547400	Flanking Active TSS	Pancreas	Pancrea
6	chr11:65546400-65547400	Transcr. at gene 5' and 3'	Spleen	Spleen
7	chr11:65546400-65547600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:65546600-65547600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:65546600-65547600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr11:65546800-65547400	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
11	chr11:65546800-65547400	Flanking Active TSS	GM12878-XiMat	blood
12	chr11:65546800-65547400	Flanking Active TSS	Hela-S3	cervix
13	chr11:65546800-65547400	Flanking Active TSS	HUVEC	blood vessel
14	chr11:65546800-65547400	Transcr. at gene 5' and 3'	NHLF	lung
15	chr11:65546800-65547600	Flanking Active TSS	Brain Angular Gyrus	brain
16	chr11:65546800-65547600	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr11:65546800-65547600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
18	chr11:65546800-65547600	Flanking Active TSS	Placenta	Placenta
19	chr11:65546800-65547600	Flanking Active TSS	HMEC	breast
20	chr11:65546800-65548000	Transcr. at gene 5' and 3'	Dnd41	blood
21	chr11:65546800-65548200	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr11:65546800-65549000	Active TSS	HSMM	muscle
23	chr11:65547000-65547400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:65547000-65547400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:65547000-65547400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:65547000-65547400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:65547000-65547400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr11:65547000-65547400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:65547000-65547400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:65547000-65547400	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr11:65547000-65547400	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr11:65547000-65547400	Flanking Active TSS	Esophagus	oesophagus
33	chr11:65547000-65547400	Flanking Active TSS	Left Ventricle	heart
34	chr11:65547000-65547400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
35	chr11:65547000-65547400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
36	chr11:65547000-65547400	Enhancers	Small Intestine	intestine
37	chr11:65547000-65547400	Transcr. at gene 5' and 3'	A549	lung
38	chr11:65547000-65547400	Flanking Active TSS	HepG2	liver
39	chr11:65547000-65547400	Flanking Active TSS	K562	blood
40	chr11:65547000-65547400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr11:65547000-65547400	Flanking Active TSS	NHDF-Ad	bronchial
42	chr11:65547000-65547400	Flanking Active TSS	NHEK	skin
43	chr11:65547000-65547400	Flanking Active TSS	Osteobl	bone
44	chr11:65547000-65547600	Enhancers	Primary hematopoietic stem cells	blood
45	chr11:65547000-65547600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr11:65547000-65547600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:65547000-65547600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr11:65547000-65547600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr11:65547000-65547600	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr11:65547000-65547600	Flanking Active TSS	Liver	Liver

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