Variant report

Variant	rs10195281
Chromosome Location	chr2:55848021-55848022
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:5)
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	POLR2A	chr2:55847510-55848770	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:55847990-55848102	HUVEC	blood vessel:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
2	chr2:55818262..55820533-chr2:55847496..55849858,2	MCF-7	breast:
3	chr2:55843280..55846696-chr2:55847912..55852861,6	MCF-7	breast:
4	chr2:55847894..55850021-chr2:55856235..55857780,2	MCF-7	breast:
5	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:

No data

Variant related genes	Relation type
SMEK2	TF binding region
ENSG00000138041	Chromatin interaction
ENSG00000115355	Chromatin interaction
ENSG00000272606	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10172181	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10172506	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10173150	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10182131	0.83[AMR][1000 genomes]
rs10200159	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10203953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10204169	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1045920	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10496044	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11676573	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11902712	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12615063	0.83[AMR][1000 genomes]
rs12616502	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12616982	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12622830	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12623625	0.83[AMR][1000 genomes]
rs12989898	0.82[AFR][1000 genomes]
rs13382187	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13383352	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13399762	0.88[AMR][1000 genomes]
rs13400946	0.83[AMR][1000 genomes]
rs13407344	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13420929	0.83[AMR][1000 genomes]
rs13428382	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13428486	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13430684	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17047094	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17047119	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2867964	0.83[AMR][1000 genomes]
rs3748955	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545507	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545508	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6545509	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545510	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545512	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6545513	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6712314	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6717574	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6725101	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6736996	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6739788	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6745430	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6760959	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs730884	0.84[AFR][1000 genomes]
rs736345	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs744514	0.86[AFR][1000 genomes]
rs7558127	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7567115	0.83[AMR][1000 genomes]
rs7574398	0.89[AFR][1000 genomes]
rs7575906	0.83[AMR][1000 genomes]
rs7582174	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7586115	0.83[AMR][1000 genomes]
rs7586124	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7586366	0.83[AMR][1000 genomes]
rs7594212	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7594497	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9309267	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9309268	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9636439	0.81[AFR][1000 genomes]
rs9808054	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:55846600-55848600	Weak transcription	Esophagus	oesophagus
4	chr2:55846600-55848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:55846600-55849000	Enhancers	Colon Smooth Muscle	Colon
6	chr2:55846600-55850400	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr2:55846600-55851600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:55846600-55852000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:55846600-55859400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:55846600-55861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:55846600-55862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
14	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:55846800-55848400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:55846800-55848600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:55846800-55848600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:55846800-55848600	Weak transcription	Fetal Brain Female	brain
20	chr2:55846800-55848800	Enhancers	Adipose Nuclei	Adipose
21	chr2:55846800-55848800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:55846800-55848800	Enhancers	Pancreas	Pancrea
23	chr2:55846800-55850400	Enhancers	Liver	Liver
24	chr2:55846800-55851200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr2:55846800-55853000	Weak transcription	A549	lung
26	chr2:55846800-55858200	Weak transcription	HSMM	muscle
27	chr2:55846800-55862000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:55846800-55862000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:55846800-55862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:55846800-55862600	Weak transcription	NHDF-Ad	bronchial
31	chr2:55846800-55863400	Weak transcription	HSMMtube	muscle
32	chr2:55846800-55863400	Weak transcription	NHLF	lung
33	chr2:55846800-55863800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:55847000-55849400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:55847000-55852600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr2:55847200-55849200	Weak transcription	Ovary	ovary
38	chr2:55847400-55848400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:55847400-55848600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:55847400-55848800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:55847400-55849200	Genic enhancers	Lung	lung
42	chr2:55847400-55852400	Weak transcription	HMEC	breast
43	chr2:55847400-55852800	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr2:55847400-55859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:55847400-55862200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:55847600-55848400	Weak transcription	Fetal Lung	lung
48	chr2:55847600-55848400	Weak transcription	Placenta	Placenta
49	chr2:55847600-55848600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:55847600-55848600	Enhancers	Primary T cells from cord blood	blood

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