Variant report

Variant	rs1151017
Chromosome Location	chr12:32259587-32259588
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	TCF12	chr12:32259285-32260142	ECC-1	luminal epithelium:	n/a	chr12:32259813-32259823 chr12:32259311-32259321
2	SMC3	chr12:32259402-32260164	Hela-S3	cervix:	n/a	chr12:32259600-32259614 chr12:32259992-32260002 chr12:32260107-32260114 chr12:32259722-32259732
3	MYC	chr12:32259470-32260080	MCF10A-Er-Src	breast:	n/a	chr12:32259744-32259753
4	CTCF	chr12:32259580-32259730	AG04450	lung:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259600-32259613
5	MYC	chr12:32259162-32260256	A549	lung:	n/a	chr12:32259462-32259471 chr12:32259744-32259753
6	POLR2A	chr12:32259424-32260179	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:32259525-32260352	Hela-S3	cervix:	n/a	n/a
8	CHD1	chr12:32259533-32260033	GM12878	blood:	n/a	chr12:32259718-32259728
9	POLR2A	chr12:32259385-32260019	K562	blood:	n/a	n/a
10	CTCF	chr12:32259560-32259710	HFF-Myc	foreskin:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259600-32259613
11	TAF1	chr12:32259439-32260332	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr12:32259520-32259670	HCM	heart:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259600-32259613
13	RFX5	chr12:32259531-32259996	HepG2	liver:	n/a	n/a
14	CTCF	chr12:32259560-32259710	HAc	cerebellar:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259600-32259613
15	ELF1	chr12:32259105-32260562	GM12878	blood:	n/a	chr12:32260111-32260123 chr12:32259691-32259703 chr12:32259948-32259960 chr12:32259945-32259957 chr12:32259518-32259530
16	MAX	chr12:32259229-32260546	K562	blood:	n/a	chr12:32259462-32259471 chr12:32259744-32259753
17	CTCF	chr12:32259520-32259670	HL-60	blood:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259600-32259613
18	CTCF	chr12:32259580-32259730	AG09309	skin:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259600-32259613
19	POLR2A	chr12:32259344-32260148	A549	lung:	n/a	n/a
20	CTCF	chr12:32259508-32259897	MCF-7	breast:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259723-32259733 chr12:32259600-32259613 chr12:32259722-32259735
21	TAF1	chr12:32259509-32260615	H1-neurons	neurons:	n/a	n/a
22	CTCF	chr12:32259507-32259845	NHEK	skin:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259723-32259733 chr12:32259600-32259613 chr12:32259722-32259735
23	EGR1	chr12:32259297-32259949	MCF-7	breast:	n/a	chr12:32259460-32259473 chr12:32259517-32259531 chr12:32259520-32259533 chr12:32259521-32259530 chr12:32259520-32259530 chr12:32259519-32259533 chr12:32259521-32259531 chr12:32259519-32259534 chr12:32259520-32259533 chr12:32259520-32259533 chr12:32259521-32259532 chr12:32259515-32259537 chr12:32259520-32259533
24	RAD21	chr12:32259300-32260008	H1-hESC	embryonic stem cell:	n/a	chr12:32259722-32259732 chr12:32259806-32259820 chr12:32259792-32259806 chr12:32259602-32259616 chr12:32259600-32259614
25	YY1	chr12:32259367-32260255	HepG2	liver:	n/a	chr12:32259947-32259961 chr12:32260056-32260068 chr12:32259550-32259561 chr12:32259950-32259964 chr12:32259720-32259729
26	TEAD4	chr12:32259428-32261252	K562	blood:	n/a	n/a
27	STAT1	chr12:32259517-32260159	GM12878	blood:	n/a	n/a
28	CTCF	chr12:32259520-32259670	HEK293	kidney:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259600-32259613
29	TBL1XR1	chr12:32259387-32260083	K562	blood:	n/a	n/a
30	ZNF263	chr12:32259205-32261183	HEK293-T-REx	kidney:	n/a	chr12:32259812-32259833 chr12:32259509-32259518
31	TAF7	chr12:32259304-32260522	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr12:32259268-32260139	HUVEC	blood vessel:	n/a	n/a
33	CTCF	chr12:32259411-32259795	A549	lung:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259723-32259733 chr12:32259600-32259613 chr12:32259722-32259735
34	CTCF	chr12:32259540-32259690	GM12870	blood:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259600-32259613
35	EGR1	chr12:32259092-32260049	HCT-116	colon:	n/a	chr12:32259460-32259473 chr12:32259517-32259531 chr12:32259520-32259533 chr12:32259521-32259530 chr12:32259520-32259530 chr12:32259519-32259533 chr12:32259521-32259531 chr12:32259519-32259534 chr12:32259520-32259533 chr12:32259520-32259533 chr12:32259521-32259532 chr12:32259515-32259537 chr12:32259520-32259533
36	POLR2A	chr12:32259570-32260009	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr12:32259293-32260577	ECC-1	luminal epithelium:	n/a	n/a
38	CTCF	chr12:32259408-32259775	H1-hESC	embryonic stem cell:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259723-32259733 chr12:32259600-32259613 chr12:32259722-32259735
39	IRF1	chr12:32259468-32259952	K562	blood:	n/a	chr12:32259716-32259730
40	POLR2A	chr12:32259441-32260258	GM12892	blood:	n/a	n/a
41	CHD2	chr12:32259307-32260540	GM12878	blood:	n/a	chr12:32259718-32259728 chr12:32260031-32260041
42	POLR2A	chr12:32259344-32260164	PBDE	blood:	n/a	n/a
43	HA-E2F1	chr12:32259044-32260159	MCF-7	breast:	n/a	chr12:32259720-32259729 chr12:32260116-32260125 chr12:32259516-32259528 chr12:32259717-32259729
44	CTCF	chr12:32259513-32259851	GM19240	blood:	n/a	chr12:32259599-32259615 chr12:32259598-32259616 chr12:32259723-32259733 chr12:32259600-32259613 chr12:32259722-32259735
45	MEF2A	chr12:32259418-32260189	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:32259489-32260064	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr12:32259375-32260134	GM12878	blood:	n/a	n/a
48	EP300	chr12:32259567-32259798	GM12878	blood:	n/a	chr12:32259725-32259741 chr12:32259729-32259745
49	REST	chr12:32259537-32260246	A549	lung:	n/a	chr12:32259715-32259725
50	POLR2A	chr12:32259372-32260002	U87	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:32259544-32259594	RPTEC	kidney:	n/a
2	chr12:32259544-32259594	PFSK-1	brain:	n/a
3	chr12:32259544-32259594	ECC-1	luminal epithelium:	n/a
4	chr12:32259544-32259594	HCF	heart:	n/a
5	chr12:32259544-32259594	HepG2	liver:	n/a
6	chr12:32259544-32259594	PrEC	prostate:	n/a
7	chr12:32259544-32259594	NH-A	brain:	n/a
8	chr12:32259544-32259594	BE2_C	brain:	n/a
9	chr12:32259544-32259594	HUVEC	blood vessel:	n/a
10	chr12:32259544-32259594	HIPEpiC	eye:	n/a
11	chr12:32259544-32259594	BJ	skin:	n/a
12	chr12:32259544-32259594	AG09309	skin:	n/a
13	chr12:32259544-32259594	AG04449	skin:	fetal
14	chr12:32259544-32259594	K562	blood:	n/a
15	chr12:32259544-32259594	HEK293	kidney:	embryo
16	chr12:32259544-32259594	NHDF-neo	bronchial:	n/a
17	chr12:32259544-32259594	Jurkat	blood:	n/a
18	chr12:32259544-32259594	HCPEpiC	choroid plexus:	n/a
19	chr12:32259544-32259594	MCF10A-Er-Src	breast:	n/a
20	chr12:32259544-32259594	ProgFib	skin:	n/a
21	chr12:32259544-32259594	GM06990	blood:	n/a
22	chr12:32259544-32259594	AoSMC	blood vessel:	n/a
23	chr12:32259544-32259594	Caco-2	colon:	n/a
24	chr12:32259544-32259594	ovcar-3	ovarian:	n/a
25	chr12:32259544-32259594	HEEpiC	esophagus:	n/a
26	chr12:32259544-32259594	MCF-7	breast:	n/a
27	chr12:32259544-32259594	T-47D	breast:	n/a
28	chr12:32259544-32259594	H1-hESC	embryonic stem cell:	embryo
29	chr12:32259544-32259594	HRPEpiC	eye:	n/a
30	chr12:32259544-32259594	Hepatocyte	liver:	n/a
31	chr12:32259544-32259594	HRCEpiC	kidney:	n/a
32	chr12:32259544-32259594	HMEC	breast:	n/a
33	chr12:32259544-32259594	GM12891	blood:	n/a
34	chr12:32259544-32259594	HCM	heart:	n/a
35	chr12:32259544-32259594	HCT-116	colon:	n/a
36	chr12:32259544-32259594	GM19239	blood:	n/a
37	chr12:32259544-32259594	PANC-1	pancreas:	n/a
38	chr12:32259544-32259594	NB4	blood:	n/a
39	chr12:32259544-32259594	HL-60	blood:	n/a
40	chr12:32259544-32259594	LNCaP	prostate:	n/a
41	chr12:32259544-32259594	AG09319	gingival:	n/a
42	chr12:32259544-32259594	SKMC	muscle:	n/a
43	chr12:32259544-32259594	HPAEpiC	pulmonary alveolar:	n/a
44	chr12:32259544-32259594	HAEpiC	amniotic membrane:	n/a
45	chr12:32259544-32259594	HRE	kidney:	n/a
46	chr12:32259544-32259594	IMR90	lung:	fetal
47	chr12:32259544-32259594	CMK	blood:	n/a
48	chr12:32259544-32259594	HNPCEpiC	eye:	n/a
49	chr12:32259544-32259594	A549	lung:	n/a
50	chr12:32259544-32259594	Hela-S3	cervix:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31880708..31883036-chr12:32258362..32261321,3	K562	blood:
2	chr12:32257278..32259683-chr12:32278967..32281640,2	MCF-7	breast:

Variant related genes	Relation type
BICD1	TF binding region
BICD1	CpG island
ENSG00000151743	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1151016	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1260708	0.84[ASN][1000 genomes]
rs1261166	0.81[ASN][1000 genomes]
rs1618256	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1631036	0.87[ASN][1000 genomes]
rs1673857	0.89[ASN][1000 genomes]
rs1673858	0.89[ASN][1000 genomes]
rs1716941	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1798260	0.86[ASN][1000 genomes]
rs2683491	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[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	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv976030	chr12:32153446-32307541	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv983498	chr12:32153446-32388092	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription 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	10 gene(s)	inside rSNPs	diseases
6	nsv898969	chr12:32224948-32375677	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1042317	chr12:32228872-32316774	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1041733	chr12:32247427-32312547	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32258400-32261600	Active TSS	Brain Germinal Matrix	brain
2	chr12:32258800-32259600	Flanking Active TSS	Dnd41	blood
3	chr12:32258800-32260200	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr12:32258800-32260600	Active TSS	Colon Smooth Muscle	Colon
5	chr12:32258800-32260800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr12:32258800-32260800	Active TSS	Fetal Kidney	kidney
7	chr12:32258800-32261400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:32258800-32262400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:32258800-32263000	Active TSS	Fetal Brain Female	brain
10	chr12:32259000-32259600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr12:32259000-32259600	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr12:32259000-32259600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr12:32259000-32259600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:32259000-32259800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr12:32259000-32260200	Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr12:32259000-32260200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:32259000-32260200	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr12:32259000-32260400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:32259000-32260400	Active TSS	Brain Anterior Caudate	brain
20	chr12:32259000-32260400	Active TSS	Fetal Muscle Trunk	muscle
21	chr12:32259000-32260400	Active TSS	Fetal Muscle Leg	muscle
22	chr12:32259000-32260400	Active TSS	Rectal Smooth Muscle	rectum
23	chr12:32259000-32260800	Active TSS	Brain Cingulate Gyrus	brain
24	chr12:32259000-32261200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:32259000-32261200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:32259000-32261400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr12:32259000-32261600	Active TSS	Muscle Satellite Cultured Cells	--
28	chr12:32259000-32261600	Active TSS	Brain Angular Gyrus	brain
29	chr12:32259000-32261800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:32259000-32261800	Active TSS	H9 Cell Line	embryonic stem cell
31	chr12:32259000-32261800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:32259000-32261800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr12:32259000-32261800	Active TSS	Thymus	Thymus
34	chr12:32259000-32261800	Active TSS	HSMM	muscle
35	chr12:32259000-32261800	Active TSS	HSMMtube	muscle
36	chr12:32259000-32261800	Active TSS	NHLF	lung
37	chr12:32259000-32262000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:32259000-32262000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:32259000-32262000	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr12:32259000-32262400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:32259000-32262400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:32259000-32263200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr12:32259000-32263200	Active TSS	Ovary	ovary
44	chr12:32259200-32259600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
45	chr12:32259200-32259600	Flanking Active TSS	Liver	Liver
46	chr12:32259200-32259600	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
47	chr12:32259200-32259600	Flanking Active TSS	GM12878-XiMat	blood
48	chr12:32259200-32259800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:32259200-32259800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:32259200-32260000	Weak transcription	Fetal Heart	heart

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