Variant report

Variant	rs2728678
Chromosome Location	chr12:32551153-32551154
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr12:32550617-32551188	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr12:32551140-32551290	HBMEC	blood vessel:	n/a	n/a
3	EP300	chr12:32550321-32551213	ECC-1	luminal epithelium:	n/a	chr12:32550480-32550494
4	TCF12	chr12:32550475-32551252	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr12:32550455-32551179	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr12:32550328-32551186	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr12:32550538-32551154	ECC-1	luminal epithelium:	n/a	n/a
8	FOXM1	chr12:32550363-32551194	ECC-1	luminal epithelium:	n/a	n/a
9	NFIC	chr12:32550369-32551261	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr12:32550403-32551180	ECC-1	luminal epithelium:	n/a	n/a
11	GATA1	chr12:32551026-32551504	PBDE	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32550852..32553049-chr12:32831118..32832629,2	MCF-7	breast:
2	chr12:32551025..32552744-chr12:32831132..32833604,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000207176	TF binding region
FGD4	TF binding region
ENSG00000087470	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1045751	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10771942	0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10771943	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10844197	0.96[ASN][1000 genomes]
rs10844198	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1128591	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs167806	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs186568	0.87[ASN][1000 genomes]
rs188978	0.94[ASN][1000 genomes]
rs188979	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2062600	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[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	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2455004	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2632330	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2632337	0.89[ASN][1000 genomes]
rs2632363	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2651365	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2651366	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2651367	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2651368	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2651369	0.80[ASN][1000 genomes]
rs2651371	0.82[ASN][1000 genomes]
rs2651377	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2728675	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2728676	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2728679	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2728689	0.90[ASN][1000 genomes]
rs2728690	0.89[ASN][1000 genomes]
rs2733683	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2733694	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2733696	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2733698	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2733703	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2733704	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2733705	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2931554	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs325418	0.93[ASN][1000 genomes]
rs325419	0.94[ASN][1000 genomes]
rs325420	0.93[ASN][1000 genomes]
rs325421	0.92[ASN][1000 genomes]
rs325423	0.84[ASN][1000 genomes]
rs325424	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs325425	0.85[JPT][hapmap]
rs325426	0.84[JPT][hapmap]
rs4931622	0.87[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	0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7312698	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7315762	0.87[ASN][1000 genomes]
rs7315797	0.86[ASN][1000 genomes]
rs7958506	0.85[JPT][hapmap]
rs7963401	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32544200-32551600	Weak transcription	Gastric	stomach
2	chr12:32544200-32551800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:32544400-32551800	Weak transcription	Ovary	ovary
4	chr12:32544400-32551800	Weak transcription	HUVEC	blood vessel
5	chr12:32544600-32551200	Weak transcription	Fetal Intestine Large	intestine
6	chr12:32544600-32551600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:32548400-32551600	Weak transcription	A549	lung
8	chr12:32550000-32551200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr12:32550200-32551600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:32550400-32551400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr12:32550400-32551400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr12:32550400-32551400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr12:32550600-32551400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr12:32550600-32551400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr12:32550600-32551400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:32550600-32551600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:32550600-32551600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:32550600-32551600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:32550600-32551800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr12:32550600-32551800	Enhancers	Brain Cingulate Gyrus	brain
21	chr12:32550800-32551200	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr12:32550800-32551400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr12:32550800-32551400	Enhancers	H9 Cell Line	embryonic stem cell
24	chr12:32550800-32551800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:32550800-32551800	Enhancers	Pancreas	Pancrea
26	chr12:32550800-32552200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr12:32551000-32551200	Weak transcription	Stomach Mucosa	stomach
28	chr12:32551000-32551600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:32551000-32551600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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