Variant report

Variant	rs461942
Chromosome Location	chr5:70885618-70885619
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:8)
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	RUNX3	chr5:70885613-70886184	GM12878	blood:	n/a	n/a
2	MXI1	chr5:70884576-70885666	SK-N-SH	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:70881870..70884694-chr5:70885301..70891902,7	MCF-7	breast:
2	chr5:70881577..70886916-chr5:70891929..70900227,16	MCF-7	breast:
3	chr5:70870301..70875589-chr5:70883224..70887581,4	MCF-7	breast:
4	chr5:70882648..70886012-chr5:70920531..70924466,3	K562	blood:
5	chr5:70880133..70886735-chr5:70895650..70901637,10	MCF-7	breast:
6	chr5:70885597..70888590-chr5:70888980..70891724,4	MCF-7	breast:
7	chr5:70883878..70887580-chr5:70891405..70894928,5	K562	blood:
8	chr5:70883251..70886427-chr5:70928765..70931034,4	MCF-7	breast:

No data

Variant related genes	Relation type
MCCC2	TF binding region
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10057258	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10079014	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1017225	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10942548	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12187886	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12652916	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13169095	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13182226	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13183892	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs156756	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs157192	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs157193	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs166758	0.86[AMR][1000 genomes]
rs16871757	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs169406	0.81[AMR][1000 genomes]
rs1990996	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2059196	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs276589	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs277927	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277941	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs277946	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277947	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs277955	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs277977	0.85[AMR][1000 genomes]
rs277982	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs277983	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs277984	0.82[AMR][1000 genomes]
rs277987	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs277988	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs277989	0.81[AMR][1000 genomes]
rs277990	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs277991	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs277992	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs277993	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs277994	0.86[AMR][1000 genomes]
rs277998	0.86[AMR][1000 genomes]
rs279289	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs282357	0.86[AMR][1000 genomes]
rs368462	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3761966	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs388918	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs411050	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs412766	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs421128	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs457889	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs458829	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4602607	0.82[EUR][1000 genomes]
rs462534	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464639	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs467880	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs467883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs468010	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs468796	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4703987	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4704050	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs561139	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs617876	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67735897	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6872978	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs875136	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9885334	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70883800-70886000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:70883800-70889000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:70883800-70889800	Weak transcription	Lung	lung
4	chr5:70883800-70892000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:70883800-70892000	Weak transcription	NH-A	brain
6	chr5:70883800-70895400	Weak transcription	HSMMtube	muscle
7	chr5:70883800-70896400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:70883800-70906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:70883800-70916400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:70884000-70885800	Enhancers	Primary B cells from cord blood	blood
11	chr5:70884000-70886200	Enhancers	Primary B cells from peripheral blood	blood
12	chr5:70884000-70886200	Enhancers	Pancreas	Pancrea
13	chr5:70884000-70886400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:70884000-70886600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr5:70884000-70886600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:70884000-70887000	Enhancers	Adipose Nuclei	Adipose
17	chr5:70884000-70887800	Weak transcription	Fetal Stomach	stomach
18	chr5:70884000-70889800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr5:70884000-70889800	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:70884000-70891400	Weak transcription	Fetal Thymus	thymus
21	chr5:70884000-70891600	Weak transcription	Fetal Brain Female	brain
22	chr5:70884000-70892000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr5:70884000-70892000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:70884000-70892200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:70884000-70892400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:70884000-70892400	Weak transcription	Thymus	Thymus
27	chr5:70884000-70892800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:70884000-70892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:70884000-70892800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:70884000-70893000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:70884000-70895400	Weak transcription	HSMM	muscle
32	chr5:70884000-70895400	Weak transcription	HUVEC	blood vessel
33	chr5:70884000-70896200	Weak transcription	Fetal Kidney	kidney
34	chr5:70884000-70896200	Weak transcription	NHDF-Ad	bronchial
35	chr5:70884000-70896200	Weak transcription	NHLF	lung
36	chr5:70884000-70900000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:70884200-70885800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr5:70884200-70885800	Flanking Active TSS	HepG2	liver
39	chr5:70884200-70887000	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr5:70884200-70889000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr5:70884200-70889200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:70884200-70893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:70884400-70885800	Enhancers	Brain Cingulate Gyrus	brain
44	chr5:70884400-70886000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:70884400-70886000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:70884400-70886200	Enhancers	Small Intestine	intestine
47	chr5:70884400-70886400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr5:70884400-70889400	Weak transcription	Fetal Intestine Small	intestine
49	chr5:70884400-70892000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr5:70884400-70892000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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