Variant report

Variant	rs2248745
Chromosome Location	chr1:153509892-153509893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCB1	chr1:153507275-153510073	Hela-S3	cervix:	n/a	n/a
2	TCF12	chr1:153505017-153510005	A549	lung:	n/a	chr1:153505279-153505288 chr1:153508760-153508770

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153507285..153510261-chr1:153579792..153582160,3	MCF-7	breast:
2	chr1:153506339..153510656-chr1:153517043..153519160,4	K562	blood:
3	chr1:153509159..153511190-chr1:153606229..153608319,3	K562	blood:
4	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
5	chr1:153508634..153510673-chr1:153516202..153519160,2	K562	blood:
6	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
7	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
8	chr1:153508608..153510769-chr1:153600428..153603319,2	K562	blood:
9	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
10	chr1:153508630..153510790-chr1:153606132..153607908,2	K562	blood:
11	chr1:153508488..153510083-chr1:153537210..153538800,2	K562	blood:
12	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:

No data

Variant related genes	Relation type
S100A6	TF binding region
ENSG00000272030	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000189334	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs17695220	0.83[AMR][1000 genomes]
rs2094217	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094737	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094738	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2262587	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2339696	0.83[AMR][1000 genomes]
rs2480695	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480696	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427870	0.93[ASN][1000 genomes]
rs28464843	0.86[AMR][1000 genomes]
rs28483109	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762262	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4017737	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272569	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4430277	0.81[EUR][1000 genomes]
rs477339	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845351	0.83[EUR][1000 genomes]
rs4845352	0.84[EUR][1000 genomes]
rs532652	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs550597	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs552446	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585215	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587743	0.83[AMR][1000 genomes]
rs659403	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659755	0.83[AMR][1000 genomes]
rs7518306	0.83[EUR][1000 genomes]
rs7520093	0.86[AMR][1000 genomes]
rs7534343	0.86[AMR][1000 genomes]
rs7534347	0.86[AMR][1000 genomes]
rs9426945	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427239	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427287	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153508600-153511600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:153508800-153512600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:153509000-153510000	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr1:153509000-153510200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr1:153509000-153510600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:153509000-153511200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:153509000-153511400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:153509200-153510000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:153509200-153510000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:153509200-153510400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:153509200-153510600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:153509200-153510600	Enhancers	Stomach Mucosa	stomach
13	chr1:153509200-153510600	Enhancers	K562	blood
14	chr1:153509200-153511000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr1:153509200-153512600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:153509200-153512600	Weak transcription	Small Intestine	intestine
17	chr1:153509200-153512800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:153509200-153514000	Enhancers	HMEC	breast
19	chr1:153509200-153515400	Weak transcription	Aorta	Aorta
20	chr1:153509200-153515600	Weak transcription	Fetal Kidney	kidney
21	chr1:153509200-153516800	Enhancers	Fetal Thymus	thymus
22	chr1:153509200-153517400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:153509400-153510000	Enhancers	Primary hematopoietic stem cells	blood
24	chr1:153509400-153510000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:153509400-153510000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:153509400-153510000	Bivalent Enhancer	HepG2	liver
27	chr1:153509400-153510200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:153509400-153510200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr1:153509400-153510400	Enhancers	Colonic Mucosa	Colon
30	chr1:153509400-153510600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:153509400-153510600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:153509400-153510600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:153509400-153510600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:153509400-153510600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:153509400-153510600	Weak transcription	Adipose Nuclei	Adipose
36	chr1:153509400-153510800	Weak transcription	NH-A	brain
37	chr1:153509400-153510800	Weak transcription	NHLF	lung
38	chr1:153509400-153511000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr1:153509400-153511000	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:153509400-153511200	Enhancers	Esophagus	oesophagus
41	chr1:153509400-153511200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:153509400-153511400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr1:153509400-153511600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:153509400-153512800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:153509400-153513000	Weak transcription	GM12878-XiMat	blood
46	chr1:153509400-153513000	Weak transcription	Osteobl	bone
47	chr1:153509400-153513200	Weak transcription	Gastric	stomach
48	chr1:153509400-153515000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:153509400-153515200	Enhancers	NHEK	skin
50	chr1:153509400-153516800	Weak transcription	Right Atrium	heart

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