Variant report

Variant	rs12095373
Chromosome Location	chr1:155827784-155827785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr1:155826212-155828027	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr1:155827661-155827991	HepG2	liver:	n/a	chr1:155827826-155827837
3	GTF3C2	chr1:155827086-155827931	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr1:155827645-155828023	K562	blood:	n/a	chr1:155827826-155827837
5	JUN	chr1:155826299-155828404	K562	blood:	n/a	chr1:155826456-155826467
6	ARID3A	chr1:155827548-155828486	HepG2	liver:	n/a	n/a
7	CEBPB	chr1:155827687-155828022	A549	lung:	n/a	chr1:155827826-155827837
8	GATA3	chr1:155827673-155827853	SH-SY5Y	brain:	n/a	n/a
9	FOXA2	chr1:155827687-155827946	HepG2	liver:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155823442..155829143-chr1:155879989..155882670,6	MCF-7	breast:
2	chr1:155821549..155823556-chr1:155827690..155829206,2	K562	blood:
3	chr1:155825653..155829252-chr1:155877943..155882760,5	MCF-7	breast:
4	chr1:155826322..155828112-chr1:156163271..156165148,2	MCF-7	breast:
5	chr1:155824896..155829386-chr1:155902844..155905236,4	MCF-7	breast:
6	chr1:155826962..155828994-chr1:155903211..155904841,2	K562	blood:
7	chr1:155827720..155829517-chr1:156180623..156183701,3	K562	blood:
8	chr1:155821775..155825361-chr1:155825507..155828654,6	MCF-7	breast:
9	chr1:155813223..155816752-chr1:155827638..155829227,3	K562	blood:
10	chr1:155825368..155829605-chr1:155879516..155883021,7	K562	blood:
11	chr1:155825171..155830547-chr1:155878470..155884979,12	K562	blood:
12	chr1:155827023..155830284-chr1:156022724..156025393,4	K562	blood:
13	chr1:155713796..155716545-chr1:155826802..155829458,2	K562	blood:

No data

Variant related genes	Relation type
SYT11	TF binding region
GON4L	TF binding region
ENSG00000116580	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000143622	Chromatin interaction
ENSG00000260238	Chromatin interaction
ENSG00000132680	Chromatin interaction
ENSG00000203761	Chromatin interaction
ENSG00000116586	Chromatin interaction
ENSG00000234937	Chromatin interaction
ENSG00000160785	Chromatin interaction
ENSG00000160783	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11264414	1.00[AMR][1000 genomes]
rs11264415	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11264418	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs12061759	1.00[AMR][1000 genomes]
rs12066633	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs12075435	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080245	1.00[MEX][hapmap]
rs12097744	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs16836999	1.00[YRI][hapmap]
rs16837068	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs1804478	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs41409345	1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs56970932	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58304308	1.00[AMR][1000 genomes]
rs6674865	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6675202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6687169	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs6692929	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs6702507	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74116434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7520381	1.00[ASW][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7523409	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7530638	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7546314	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7552711	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1003170	chr1:155762204-155836564	Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 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	chr1:155826400-155829600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:155826600-155829400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:155827000-155828800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:155827000-155828800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:155827000-155829000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:155827000-155829200	Weak transcription	Spleen	Spleen
7	chr1:155827000-155829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:155827000-155829400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:155827000-155829400	Weak transcription	Lung	lung
10	chr1:155827200-155828600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:155827200-155828600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:155827200-155828800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:155827200-155828800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:155827200-155828800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:155827200-155829000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:155827200-155829400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:155827200-155829400	Weak transcription	Gastric	stomach
18	chr1:155827200-155829600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:155827200-155829800	Flanking Active TSS	Dnd41	blood
20	chr1:155827400-155827800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:155827400-155827800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:155827400-155827800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:155827400-155827800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:155827400-155827800	Enhancers	Liver	Liver
25	chr1:155827400-155827800	Enhancers	Brain Anterior Caudate	brain
26	chr1:155827400-155827800	Enhancers	Placenta	Placenta
27	chr1:155827400-155828000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:155827400-155828000	Enhancers	Colon Smooth Muscle	Colon
29	chr1:155827400-155828000	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr1:155827400-155828200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:155827400-155828200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:155827400-155828200	Enhancers	Primary B cells from cord blood	blood
33	chr1:155827400-155828200	Weak transcription	Adipose Nuclei	Adipose
34	chr1:155827400-155828200	Enhancers	Brain Substantia Nigra	brain
35	chr1:155827400-155828200	Weak transcription	Fetal Kidney	kidney
36	chr1:155827400-155828200	Weak transcription	Small Intestine	intestine
37	chr1:155827400-155828200	Weak transcription	HMEC	breast
38	chr1:155827400-155828200	Weak transcription	HSMMtube	muscle
39	chr1:155827400-155828200	Weak transcription	NHDF-Ad	bronchial
40	chr1:155827400-155828400	Weak transcription	Fetal Brain Male	brain
41	chr1:155827400-155828400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:155827400-155828400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:155827400-155828400	Weak transcription	HSMM	muscle
44	chr1:155827400-155828600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:155827400-155828600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:155827400-155828600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:155827400-155828600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:155827400-155828600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr1:155827400-155828600	Enhancers	Primary hematopoietic stem cells	blood
50	chr1:155827400-155828600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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