Variant report

Variant	rs1667616
Chromosome Location	chr2:74348125-74348126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:74345450..74348977-chr2:74371413..74376785,7	MCF-7	breast:
2	chr2:74077294..74080205-chr2:74346163..74349130,2	K562	blood:
3	chr2:74347130..74350614-chr2:74373490..74375151,4	K562	blood:
4	chr2:74209017..74213063-chr2:74345530..74349441,7	MCF-7	breast:
5	chr2:74153590..74155495-chr2:74346048..74348829,2	MCF-7	breast:
6	chr2:74054992..74057413-chr2:74347412..74349314,2	K562	blood:
7	chr2:74346321..74348591-chr2:74373615..74376560,4	MCF-7	breast:
8	chr2:74345336..74350949-chr2:74424473..74426826,5	K562	blood:
9	chr2:74211217..74213609-chr2:74345958..74348496,2	MCF-7	breast:
10	chr2:74346058..74349268-chr2:74424477..74426947,5	K562	blood:
11	chr2:74209066..74214459-chr2:74345671..74349502,5	K562	blood:
12	chr2:74347518..74349564-chr2:74361288..74362886,2	MCF-7	breast:
13	chr2:74345940..74348146-chr2:74432915..74434982,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC073263.1-3	chr2:74345408-74349576	NONHSAT071660
2	lnc-AC073263.1-3	chr2:74347807-74349577	NONHSAT071661

No data

Variant related genes	Relation type
ENSG00000124356	Chromatin interaction
ENSG00000235499	Chromatin interaction
ENSG00000114956	Chromatin interaction
ENSG00000255989	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000163170	Chromatin interaction
ENSG00000217702	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1026150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1095970	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12465641	0.86[JPT][hapmap]
rs12996870	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13025827	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1667615	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1667622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1723283	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723284	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723290	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122290	0.86[JPT][hapmap]
rs2280642	0.86[JPT][hapmap]
rs2421753	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099822	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3099823	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108161	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108162	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34284832	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35955502	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4429500	0.82[JPT][hapmap]
rs4452177	0.85[JPT][hapmap]
rs6707619	0.83[JPT][hapmap]
rs6758220	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs702463	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs702464	0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs828841	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828843	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828845	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828846	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828848	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828850	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828864	0.89[ASN][1000 genomes]
rs828865	0.89[ASN][1000 genomes]
rs828867	0.90[JPT][hapmap]
rs828897	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs828898	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828901	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874284	chr2:74283728-74348797	Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
2	nsv874285	chr2:74283728-74355244	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74346600-74348200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:74346800-74348200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:74346800-74348200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:74346800-74348400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:74346800-74348400	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr2:74347000-74348200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:74347000-74348200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:74347000-74348200	Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr2:74347000-74348200	Active TSS	Aorta	Aorta
10	chr2:74347000-74348200	Active TSS	Brain Cingulate Gyrus	brain
11	chr2:74347000-74348200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr2:74347000-74348200	Active TSS	Ovary	ovary
13	chr2:74347000-74348200	Active TSS	Right Ventricle	heart
14	chr2:74347000-74348200	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr2:74347000-74348200	Active TSS	Stomach Smooth Muscle	stomach
16	chr2:74347000-74348200	Flanking Active TSS	HMEC	breast
17	chr2:74347000-74348200	Active TSS	NH-A	brain
18	chr2:74347000-74348200	Active TSS	NHLF	lung
19	chr2:74347200-74348200	Active TSS	Primary hematopoietic stem cells	blood
20	chr2:74347200-74348200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:74347200-74348200	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr2:74347200-74348200	Active TSS	Muscle Satellite Cultured Cells	--
23	chr2:74347200-74348200	Active TSS	Thymus	Thymus
24	chr2:74347600-74348200	Flanking Active TSS	Dnd41	blood
25	chr2:74347600-74348200	Flanking Active TSS	GM12878-XiMat	blood
26	chr2:74347800-74348200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr2:74347800-74348200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:74347800-74348200	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr2:74347800-74348200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr2:74347800-74348200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr2:74347800-74348200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:74347800-74348200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:74347800-74348200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr2:74347800-74348200	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr2:74347800-74348200	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr2:74347800-74348200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr2:74347800-74348200	Flanking Bivalent TSS/Enh	HepG2	liver
38	chr2:74347800-74348200	ZNF genes & repeats	HSMMtube	muscle
39	chr2:74347800-74348200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr2:74347800-74348200	Flanking Active TSS	Osteobl	bone
41	chr2:74347800-74348400	Flanking Active TSS	Hela-S3	cervix
42	chr2:74347800-74348400	Flanking Active TSS	NHEK	skin
43	chr2:74347800-74348600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
44	chr2:74347800-74348600	ZNF genes & repeats	Fetal Lung	lung
45	chr2:74347800-74348800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:74347800-74348800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:74347800-74348800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
48	chr2:74347800-74348800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr2:74347800-74349000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:74347800-74349000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell

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