Variant report

Variant	rs2651369
Chromosome Location	chr12:32552769-32552770
allele	C/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	CTCF	chr12:32552236-32553011	HCT-116	colon:	n/a	chr12:32552403-32552411 chr12:32552660-32552673 chr12:32552660-32552669 chr12:32552964-32552972
2	ELF1	chr12:32552103-32553120	GM12878	blood:	n/a	chr12:32552142-32552154
3	CTCF	chr12:32552533-32552777	Spleen_OC	spleen:	n/a	chr12:32552660-32552673 chr12:32552660-32552669
4	CTCF	chr12:32552282-32552955	MCF-7	breast:	n/a	chr12:32552403-32552411 chr12:32552660-32552673 chr12:32552660-32552669
5	REST	chr12:32552303-32553036	ECC-1	luminal epithelium:	n/a	chr12:32552796-32552809
6	TAF7	chr12:32552067-32553519	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:32552031-32553174	MCF-7	breast:	n/a	n/a
8	E2F6	chr12:32552052-32553121	A549	lung:	n/a	chr12:32552412-32552421 chr12:32552269-32552284 chr12:32552687-32552698 chr12:32552238-32552248 chr12:32552225-32552240
9	POLR2A	chr12:32552255-32553044	H1-neurons	neurons:	n/a	n/a
10	CTCF	chr12:32552459-32552797	MCF-7	breast:	n/a	chr12:32552660-32552673 chr12:32552660-32552669
11	MAZ	chr12:32552070-32553389	Hela-S3	cervix:	n/a	chr12:32552147-32552157
12	POLR2A	chr12:32552033-32552924	A549	lung:	n/a	n/a
13	TEAD4	chr12:32551849-32553556	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr12:32551981-32553421	MCF10A-Er-Src	breast:	n/a	n/a
15	MAX	chr12:32551922-32553094	A549	lung:	n/a	chr12:32552147-32552157
16	TAF1	chr12:32552107-32553483	ECC-1	luminal epithelium:	n/a	n/a
17	ELF1	chr12:32552280-32553141	MCF-7	breast:	n/a	n/a
18	CTCF	chr12:32552640-32552790	RPTEC	kidney:	n/a	chr12:32552660-32552673 chr12:32552660-32552669
19	POLR2A	chr12:32551778-32553420	Hela-S3	cervix:	n/a	n/a
20	BRCA1	chr12:32552404-32552930	Hela-S3	cervix:	n/a	n/a
21	GABPA	chr12:32552498-32553056	K562	blood:	n/a	chr12:32552906-32552915
22	CREB1	chr12:32552177-32552959	K562	blood:	n/a	n/a
23	POLR2A	chr12:32552643-32552910	A549	lung:	n/a	n/a
24	ZBTB7A	chr12:32551770-32553171	ECC-1	luminal epithelium:	n/a	n/a
25	SP4	chr12:32552334-32552791	H1-hESC	embryonic stem cell:	n/a	chr12:32552650-32552666
26	NFIC	chr12:32551624-32553415	ECC-1	luminal epithelium:	n/a	n/a
27	REST	chr12:32552111-32553082	H1-neurons	neurons:	n/a	chr12:32552796-32552809
28	POLR2A	chr12:32552187-32552887	HUVEC	blood vessel:	n/a	n/a
29	GABPA	chr12:32552228-32553343	MCF-7	breast:	n/a	chr12:32552906-32552915
30	CTCF	chr12:32552479-32552795	Gliobla	brain:	n/a	chr12:32552660-32552673 chr12:32552660-32552669
31	TAF7	chr12:32552026-32552896	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr12:32552386-32552845	H1-hESC	embryonic stem cell:	n/a	chr12:32552403-32552411 chr12:32552660-32552673 chr12:32552660-32552669
33	POLR2A	chr12:32552119-32553026	ProgFib	skin:	n/a	n/a
34	CCNT2	chr12:32552175-32552976	K562	blood:	n/a	n/a
35	RCOR1	chr12:32552109-32552803	K562	blood:	n/a	n/a
36	SIN3AK20	chr12:32552261-32553513	MCF-7	breast:	n/a	n/a
37	TCF7L2	chr12:32552412-32552827	PANC-1	pancreas:	n/a	n/a
38	TCF12	chr12:32551771-32553090	A549	lung:	n/a	chr12:32552166-32552173 chr12:32552936-32552943 chr12:32552871-32552881
39	CTCF	chr12:32552434-32552801	A549	lung:	n/a	chr12:32552660-32552673 chr12:32552660-32552669
40	CTCF	chr12:32552509-32552775	H1-hESC	embryonic stem cell:	n/a	chr12:32552660-32552673 chr12:32552660-32552669
41	MYC	chr12:32552428-32552814	MCF-7	breast:	n/a	n/a
42	CHD2	chr12:32552448-32553561	H1-hESC	embryonic stem cell:	n/a	n/a
43	HDAC2	chr12:32552423-32552821	HepG2	liver:	n/a	n/a
44	RAD21	chr12:32552456-32552797	A549	lung:	n/a	n/a
45	TAF1	chr12:32552018-32553517	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr12:32552020-32553335	Hela-S3	cervix:	n/a	n/a
47	MXI1	chr12:32552064-32552837	Hela-S3	cervix:	n/a	n/a
48	YY1	chr12:32552229-32552842	K562	blood:	n/a	chr12:32552274-32552288 chr12:32552230-32552241
49	CTCF	chr12:32552167-32553319	A549	lung:	n/a	chr12:32552403-32552411 chr12:32552660-32552673 chr12:32552660-32552669 chr12:32552964-32552972
50	TCF12	chr12:32551550-32553633	ECC-1	luminal epithelium:	n/a	chr12:32552166-32552173 chr12:32552936-32552943 chr12:32552871-32552881

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:32552765-32552815	GM12891	blood:	n/a
2	chr12:32552765-32552815	HAEpiC	amniotic membrane:	n/a
3	chr12:32552765-32552815	NH-A	brain:	n/a
4	chr12:32552765-32552815	HEK293	kidney:	embryo
5	chr12:32552765-32552815	K562	blood:	n/a
6	chr12:32552765-32552815	HUVEC	blood vessel:	n/a
7	chr12:32552765-32552815	SAEC	small airway:	n/a
8	chr12:32552765-32552815	A549	lung:	n/a
9	chr12:32552765-32552815	ECC-1	luminal epithelium:	n/a
10	chr12:32552765-32552815	HEEpiC	esophagus:	n/a
11	chr12:32552765-32552815	PFSK-1	brain:	n/a
12	chr12:32552765-32552815	LNCaP	prostate:	n/a
13	chr12:32552765-32552815	U87	brain:	n/a
14	chr12:32552765-32552815	Jurkat	blood:	n/a
15	chr12:32552765-32552815	HCT-116	colon:	n/a
16	chr12:32552765-32552815	Hela-S3	cervix:	n/a
17	chr12:32552765-32552815	PANC-1	pancreas:	n/a
18	chr12:32552765-32552815	HepG2	liver:	n/a
19	chr12:32552765-32552815	AG04450	lung:	fetal
20	chr12:32552765-32552815	NB4	blood:	n/a
21	chr12:32552765-32552815	SKMC	muscle:	n/a
22	chr12:32552765-32552815	HRCEpiC	kidney:	n/a
23	chr12:32552765-32552815	H1-hESC	embryonic stem cell:	embryo
24	chr12:32552765-32552815	HCF	heart:	n/a
25	chr12:32552765-32552815	MCF-7	breast:	n/a
26	chr12:32552765-32552815	AG04449	skin:	fetal
27	chr12:32552765-32552815	RPTEC	kidney:	n/a
28	chr12:32552765-32552815	CMK	blood:	n/a
29	chr12:32552765-32552815	Hepatocyte	liver:	n/a
30	chr12:32552765-32552815	SK-N-SH_RA	brain:	n/a
31	chr12:32552765-32552815	HNPCEpiC	eye:	n/a
32	chr12:32552765-32552815	ovcar-3	ovarian:	n/a
33	chr12:32552765-32552815	T-47D	breast:	n/a
34	chr12:32552765-32552815	SK-N-MC	brain:	n/a
35	chr12:32552765-32552815	AG10803	skin:	n/a
36	chr12:32552765-32552815	Caco-2	colon:	n/a
37	chr12:32552765-32552815	AG09309	skin:	n/a
38	chr12:32552765-32552815	GM06990	blood:	n/a
39	chr12:32552765-32552815	HCM	heart:	n/a
40	chr12:32552765-32552815	GM12892	blood:	n/a
41	chr12:32552765-32552815	PrEC	prostate:	n/a
42	chr12:32552765-32552815	NT2-D1	testis:	n/a
43	chr12:32552765-32552815	GM19239	blood:	n/a
44	chr12:32552765-32552815	HPAEpiC	pulmonary alveolar:	n/a
45	chr12:32552765-32552815	NHBE	bronchial:	n/a
46	chr12:32552765-32552815	HL-60	blood:	n/a
47	chr12:32552765-32552815	BE2_C	brain:	n/a
48	chr12:32552765-32552815	HIPEpiC	eye:	n/a
49	chr12:32552765-32552815	MCF10A-Er-Src	breast:	n/a
50	chr12:32552765-32552815	AG09319	gingival:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:32550852..32553049-chr12:32831118..32832629,2	MCF-7	breast:
2	chr12:32552355..32553211-chrX:77359577..77360122,2	Hela-S3	cervix:
3	chr12:32552199..32553014-chr7:48018664..48019299,2	HCT-116	colon:
4	chr12:32552095..32552992-chr19:18391097..18392504,4	Hela-S3	cervix:
5	chr12:32552467..32553163-chr2:113403051..113404044,2	Hela-S3	cervix:
6	chr12:32547740..32549812-chr12:32551795..32554175,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207176	TF binding region
FGD4	TF binding region
ENSG00000207176	CpG island
FGD4	CpG island
ENSG00000130522	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000207176	Chromatin interaction
ENSG00000087470	Chromatin interaction
ENSG00000102144	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000136273	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1055876	0.85[EUR][1000 genomes]
rs10844201	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11051969	0.84[EUR][1000 genomes]
rs11051970	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11051976	0.87[EUR][1000 genomes]
rs12228004	0.85[EUR][1000 genomes]
rs12229856	0.80[EUR][1000 genomes]
rs1500874	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1809912	0.84[EUR][1000 genomes]
rs1872829	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2088806	0.84[EUR][1000 genomes]
rs2088807	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2171373	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2243815	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2467065	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2470382	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2651360	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2651361	0.83[EUR][1000 genomes]
rs2651362	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2651363	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2651378	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2651379	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2728669	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2728671	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2728673	0.85[EUR][1000 genomes]
rs2728678	0.80[ASN][1000 genomes]
rs2728680	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2728682	0.84[EUR][1000 genomes]
rs2733682	0.82[EUR][1000 genomes]
rs325417	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6488050	0.82[EUR][1000 genomes]
rs6488051	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7296118	0.82[EUR][1000 genomes]
rs73081911	0.84[EUR][1000 genomes]
rs73084099	0.85[EUR][1000 genomes]
rs73084101	0.85[EUR][1000 genomes]
rs7309706	0.85[EUR][1000 genomes]
rs950079	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs950080	0.81[AMR][1000 genomes];0.84[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	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
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv469346	chr12:32531220-32587465	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv558188	chr12:32531220-32587465	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3324783	chr12:32551310-32553858	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	esv3427823	chr12:32551585-32553583	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2651369	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32551200-32554800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:32551600-32553000	Active TSS	Brain Angular Gyrus	brain
3	chr12:32551600-32553600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:32551600-32553800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr12:32551600-32553800	Active TSS	Rectal Smooth Muscle	rectum
6	chr12:32551600-32554200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:32551800-32552800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:32551800-32552800	Active TSS	Brain Germinal Matrix	brain
9	chr12:32551800-32552800	Enhancers	Fetal Brain Male	brain
10	chr12:32551800-32552800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
11	chr12:32551800-32552800	Active TSS	NHLF	lung
12	chr12:32551800-32553000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
13	chr12:32551800-32553000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:32551800-32553000	Active TSS	Brain Cingulate Gyrus	brain
15	chr12:32551800-32553000	Active TSS	Brain Hippocampus Middle	brain
16	chr12:32551800-32553000	Bivalent/Poised TSS	Fetal Stomach	stomach
17	chr12:32551800-32553000	Active TSS	HSMMtube	muscle
18	chr12:32551800-32553200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:32551800-32553200	Active TSS	Muscle Satellite Cultured Cells	--
20	chr12:32551800-32553400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:32551800-32553400	Active TSS	Aorta	Aorta
22	chr12:32551800-32553600	Active TSS	Brain Substantia Nigra	brain
23	chr12:32551800-32553600	Active TSS	HSMM	muscle
24	chr12:32551800-32553800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:32551800-32553800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:32551800-32553800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:32551800-32553800	Active TSS	Left Ventricle	heart
28	chr12:32551800-32554000	Active TSS	Right Ventricle	heart
29	chr12:32551800-32554200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr12:32551800-32554200	Active TSS	Ovary	ovary
31	chr12:32551800-32554400	Active TSS	H9 Cell Line	embryonic stem cell
32	chr12:32551800-32554600	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr12:32551800-32554800	Active TSS	H1 Cell Line	embryonic stem cell
34	chr12:32551800-32555200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:32552000-32552800	Active TSS	Duodenum Mucosa	Duodenum
36	chr12:32552000-32552800	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr12:32552000-32552800	Active TSS	Fetal Intestine Large	intestine
38	chr12:32552000-32552800	Active TSS	Psoas Muscle	Psoas
39	chr12:32552000-32552800	Active TSS	Stomach Smooth Muscle	stomach
40	chr12:32552000-32553000	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr12:32552000-32553000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:32552000-32553000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:32552000-32553000	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr12:32552000-32553000	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr12:32552000-32553000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr12:32552000-32553000	Active TSS	Brain Anterior Caudate	brain
47	chr12:32552000-32553000	Active TSS	GM12878-XiMat	blood
48	chr12:32552000-32553200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
49	chr12:32552000-32553200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:32552000-32553400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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