Variant report

Variant	rs2070960
Chromosome Location	chr1:228284991-228284992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228284520..228292111-chr1:228324853..228335412,14	K562	blood:
2	chr1:228283995..228287162-chr1:228352238..228356052,3	K562	blood:

miRNA name	Chromosome Location	mirBase accession
hsa-miR-3620-5p	chr1:228284986-228285007	MIMAT0022967

Variant related genes	Relation type
ENSG00000143774	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000181873	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1034792	0.84[EUR][1000 genomes]
rs1048503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916262	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10916266	0.81[ASN][1000 genomes]
rs1094603	0.81[ASN][1000 genomes]
rs11582265	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11582704	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11584499	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11589513	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1188975	0.93[EUR][1000 genomes]
rs1188977	1.00[EUR][1000 genomes]
rs12033088	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048010	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1620734	1.00[EUR][1000 genomes]
rs1745422	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2295995	0.86[EUR][1000 genomes]
rs3738680	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768329	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768330	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3820624	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270175	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41270177	0.84[EUR][1000 genomes]
rs4653897	0.84[EUR][1000 genomes]
rs57146523	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57657087	0.81[EUR][1000 genomes]
rs61825130	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61825131	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61825133	0.99[ASN][1000 genomes]
rs61825135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61825156	0.86[ASN][1000 genomes]
rs708126	0.93[EUR][1000 genomes]
rs72756204	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756209	0.81[AMR][1000 genomes]
rs822727	1.00[EUR][1000 genomes]
rs860301	1.00[EUR][1000 genomes]
rs882451	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer 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 miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 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	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:228275800-228286600	Weak transcription	Fetal Kidney	kidney
3	chr1:228276600-228285000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:228276800-228290200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:228277200-228290000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:228277600-228289200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:228278000-228289400	Genic enhancers	Pancreas	Pancrea
8	chr1:228279000-228285000	Weak transcription	HSMMtube	muscle
9	chr1:228279200-228287800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:228279600-228285600	Weak transcription	NH-A	brain
11	chr1:228279600-228289000	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr1:228280000-228285200	ZNF genes & repeats	Fetal Stomach	stomach
13	chr1:228280200-228288800	Weak transcription	Fetal Heart	heart
14	chr1:228280400-228285400	ZNF genes & repeats	Brain Germinal Matrix	brain
15	chr1:228280600-228286400	Weak transcription	Psoas Muscle	Psoas
16	chr1:228280800-228289600	Weak transcription	Small Intestine	intestine
17	chr1:228281400-228289000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:228282400-228289200	Strong transcription	NHEK	skin
19	chr1:228282600-228285000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:228282600-228285200	Weak transcription	HMEC	breast
21	chr1:228282600-228285600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:228282600-228286400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:228282600-228287200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:228282600-228288800	Strong transcription	K562	blood
25	chr1:228282600-228289000	Strong transcription	Primary T cells from cord blood	blood
26	chr1:228282800-228285000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:228282800-228285200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:228282800-228285200	Weak transcription	HUVEC	blood vessel
29	chr1:228282800-228287400	Strong transcription	GM12878-XiMat	blood
30	chr1:228282800-228287800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:228282800-228288000	Strong transcription	Brain Substantia Nigra	brain
32	chr1:228282800-228289000	Strong transcription	Fetal Lung	lung
33	chr1:228282800-228289200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:228282800-228289200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:228283000-228285000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:228283000-228285200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:228283000-228288800	Strong transcription	Dnd41	blood
38	chr1:228283000-228289000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:228283000-228289000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:228283000-228289200	Strong transcription	Brain Anterior Caudate	brain
41	chr1:228283200-228285200	Weak transcription	NHDF-Ad	bronchial
42	chr1:228283200-228288600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:228283200-228288600	Strong transcription	Fetal Intestine Large	intestine
44	chr1:228283200-228288800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:228283200-228289200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:228283200-228289200	Genic enhancers	Gastric	stomach
47	chr1:228283400-228288000	Strong transcription	A549	lung
48	chr1:228283400-228288600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:228283400-228288600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:228283400-228288800	Strong transcription	NHLF	lung

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