Variant report

Variant	rs2728676
Chromosome Location	chr12:32553149-32553150
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	TAF7	chr12:32552067-32553519	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:32552031-32553174	MCF-7	breast:	n/a	n/a
3	MAZ	chr12:32552070-32553389	Hela-S3	cervix:	n/a	chr12:32552147-32552157
4	TEAD4	chr12:32551849-32553556	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr12:32551981-32553421	MCF10A-Er-Src	breast:	n/a	n/a
6	RFX5	chr12:32553062-32553471	Hela-S3	cervix:	n/a	n/a
7	TAF1	chr12:32552107-32553483	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr12:32551778-32553420	Hela-S3	cervix:	n/a	n/a
9	SIN3AK20	chr12:32553088-32553471	H1-hESC	embryonic stem cell:	n/a	n/a
10	ZBTB7A	chr12:32551770-32553171	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr12:32551624-32553415	ECC-1	luminal epithelium:	n/a	n/a
12	GABPA	chr12:32552228-32553343	MCF-7	breast:	n/a	chr12:32552906-32552915
13	GTF2F1	chr12:32553121-32553513	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3AK20	chr12:32552261-32553513	MCF-7	breast:	n/a	n/a
15	CHD2	chr12:32552448-32553561	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAF1	chr12:32552018-32553517	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:32552020-32553335	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr12:32552167-32553319	A549	lung:	n/a	chr12:32552403-32552411 chr12:32552660-32552673 chr12:32552660-32552669 chr12:32552964-32552972
19	TCF12	chr12:32551550-32553633	ECC-1	luminal epithelium:	n/a	chr12:32552166-32552173 chr12:32552936-32552943 chr12:32552871-32552881
20	SRF	chr12:32552209-32553153	ECC-1	luminal epithelium:	n/a	chr12:32552238-32552248
21	EGR1	chr12:32551873-32553307	ECC-1	luminal epithelium:	n/a	chr12:32552188-32552197 chr12:32552233-32552243
22	ATF2	chr12:32552294-32553761	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr12:32553060-32553210	GM06990	blood:	n/a	n/a
24	CTCF	chr12:32553040-32553190	Caco-2	colon:	n/a	n/a
25	POLR2A	chr12:32552105-32553334	MCF-7	breast:	n/a	n/a
26	HDAC2	chr12:32553129-32553649	H1-hESC	embryonic stem cell:	n/a	chr12:32553612-32553626 chr12:32553158-32553172 chr12:32553613-32553627
27	JUND	chr12:32552458-32553797	H1-hESC	embryonic stem cell:	n/a	chr12:32552882-32552893
28	CTBP2	chr12:32551946-32553418	H1-hESC	embryonic stem cell:	n/a	n/a
29	EGR1	chr12:32552848-32553321	MCF-7	breast:	n/a	n/a
30	SMC3	chr12:32552070-32553431	Hela-S3	cervix:	n/a	chr12:32552663-32552673 chr12:32552607-32552621
31	CHD1	chr12:32552453-32554107	H1-hESC	embryonic stem cell:	n/a	n/a
32	GABPA	chr12:32552939-32553478	H1-hESC	embryonic stem cell:	n/a	n/a
33	CEBPB	chr12:32551931-32553167	ECC-1	luminal epithelium:	n/a	chr12:32552412-32552420
34	SIN3A	chr12:32551710-32554057	H1-hESC	embryonic stem cell:	n/a	chr12:32552230-32552241 chr12:32552960-32552971 chr12:32552074-32552088 chr12:32552940-32552951
35	SIN3AK20	chr12:32552848-32553505	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr12:32551959-32553181	A549	lung:	n/a	n/a
37	SP4	chr12:32552903-32553719	H1-hESC	embryonic stem cell:	n/a	n/a
38	NR2F2	chr12:32552487-32553236	MCF-7	breast:	n/a	n/a
39	MAX	chr12:32551825-32553597	HCT-116	colon:	n/a	chr12:32552147-32552157
40	TAF1	chr12:32551759-32553487	ECC-1	luminal epithelium:	n/a	n/a
41	YY1	chr12:32551962-32553174	ECC-1	luminal epithelium:	n/a	chr12:32552274-32552288 chr12:32552230-32552241
42	ZEB1	chr12:32551829-32553352	HepG2	liver:	n/a	chr12:32552135-32552142 chr12:32552164-32552175
43	EGR1	chr12:32552687-32553281	ECC-1	luminal epithelium:	n/a	n/a
44	YY1	chr12:32552939-32553480	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr12:32552057-32553485	Hela-S3	cervix:	n/a	chr12:32552147-32552157
46	TAF1	chr12:32551970-32553596	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:32552273-32553514	H1-hESC	embryonic stem cell:	n/a	n/a
48	MAX	chr12:32551972-32553153	HepG2	liver:	n/a	chr12:32552147-32552157
49	POLR2A	chr12:32552338-32553479	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr12:32551890-32553176	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:32552355..32553211-chrX:77359577..77360122,2	Hela-S3	cervix:
2	chr12:32552822..32553411-chr3:169306373..169306873,2	HCT-116	colon:
3	chr12:32552467..32553163-chr2:113403051..113404044,2	Hela-S3	cervix:
4	chr12:32547740..32549812-chr12:32551795..32554175,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207176	TF binding region
ENSG00000102144	Chromatin interaction
ENSG00000207176	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000237753	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1045751	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10771942	0.85[ASN][1000 genomes]
rs10771943	0.83[ASN][1000 genomes]
rs10844197	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10844198	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1128591	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs167806	0.93[ASN][1000 genomes]
rs186568	0.87[ASN][1000 genomes]
rs188978	0.94[ASN][1000 genomes]
rs188979	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2062600	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2253235	0.91[ASN][1000 genomes]
rs2253237	0.88[ASN][1000 genomes]
rs2253247	0.89[ASN][1000 genomes]
rs2450506	0.96[ASN][1000 genomes]
rs2455004	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2632330	0.92[ASN][1000 genomes]
rs2632337	0.89[ASN][1000 genomes]
rs2632363	0.90[ASN][1000 genomes]
rs2651365	0.94[ASN][1000 genomes]
rs2651366	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2651367	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2651368	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2651371	0.82[ASN][1000 genomes]
rs2651375	0.82[AFR][1000 genomes]
rs2651376	0.80[AFR][1000 genomes]
rs2651377	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2728675	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2728678	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2728679	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2728681	0.80[AFR][1000 genomes]
rs2728689	0.90[ASN][1000 genomes]
rs2728690	0.89[ASN][1000 genomes]
rs2733683	0.89[ASN][1000 genomes]
rs2733694	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2733696	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2733698	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2733703	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2733704	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2733705	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2931554	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs325418	0.93[ASN][1000 genomes]
rs325419	0.94[ASN][1000 genomes]
rs325420	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs325421	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs325423	0.84[ASN][1000 genomes]
rs325424	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4931622	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4931624	0.88[ASN][1000 genomes]
rs4931625	0.93[ASN][1000 genomes]
rs56146365	0.82[ASN][1000 genomes]
rs61927173	0.83[ASN][1000 genomes]
rs7298381	0.85[ASN][1000 genomes]
rs7312698	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7315762	0.87[ASN][1000 genomes]
rs7315797	0.86[ASN][1000 genomes]
rs7963401	0.93[ASN][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
rs2728676	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr12:32551600-32553600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:32551600-32553800	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr12:32551600-32553800	Active TSS	Rectal Smooth Muscle	rectum
5	chr12:32551600-32554200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:32551800-32553200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:32551800-32553200	Active TSS	Muscle Satellite Cultured Cells	--
8	chr12:32551800-32553400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:32551800-32553400	Active TSS	Aorta	Aorta
10	chr12:32551800-32553600	Active TSS	Brain Substantia Nigra	brain
11	chr12:32551800-32553600	Active TSS	HSMM	muscle
12	chr12:32551800-32553800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:32551800-32553800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:32551800-32553800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:32551800-32553800	Active TSS	Left Ventricle	heart
16	chr12:32551800-32554000	Active TSS	Right Ventricle	heart
17	chr12:32551800-32554200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr12:32551800-32554200	Active TSS	Ovary	ovary
19	chr12:32551800-32554400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr12:32551800-32554600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr12:32551800-32554800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr12:32551800-32555200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:32552000-32553200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
24	chr12:32552000-32553200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:32552000-32553400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:32552000-32553400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:32552000-32553600	Active TSS	Esophagus	oesophagus
28	chr12:32552000-32553600	Active TSS	Gastric	stomach
29	chr12:32552000-32553600	Active TSS	A549	lung
30	chr12:32552000-32553800	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr12:32552000-32554200	Bivalent/Poised TSS	Fetal Kidney	kidney
32	chr12:32552000-32554400	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr12:32552000-32554600	Active TSS	Stomach Mucosa	stomach
34	chr12:32552000-32554800	Active TSS	Fetal Intestine Small	intestine
35	chr12:32552000-32555200	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr12:32552000-32555400	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr12:32552200-32553200	Active TSS	Liver	Liver
38	chr12:32552200-32553200	Active TSS	Colon Smooth Muscle	Colon
39	chr12:32552200-32553200	Active TSS	Hela-S3	cervix
40	chr12:32552200-32553200	Active TSS	HepG2	liver
41	chr12:32552200-32553400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:32552200-32553400	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr12:32552200-32553400	Active TSS	Lung	lung
44	chr12:32552200-32553600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:32552200-32553600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:32552200-32553600	Active TSS	Pancreas	Pancrea
47	chr12:32552200-32553600	Active TSS	HUVEC	blood vessel
48	chr12:32552200-32553600	Active TSS	K562	blood
49	chr12:32552200-32553800	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr12:32552200-32553800	Bivalent/Poised TSS	Small Intestine	intestine

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