Variant report

Variant	rs1308520
Chromosome Location	chr1:10510682-10510683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10508493..10514342-chr1:10516490..10519388,5	K562	blood:
2	chr1:10508871..10511200-chr1:10534992..10537583,2	K562	blood:
3	chr1:10498763..10502281-chr1:10507283..10512164,5	K562	blood:
4	chr1:10508957..10511140-chr1:10530246..10532667,2	K562	blood:
5	chr1:10490085..10492364-chr1:10508772..10511442,3	K562	blood:

Variant related genes	Relation type
ENSG00000271989	Chromatin interaction
ENSG00000203469	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000175279	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10864455	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10864456	0.91[ASN][1000 genomes]
rs1188526	0.92[CHB][hapmap]
rs1188530	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1307489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1307490	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1307493	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1307494	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1307497	0.82[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1411402	0.84[CHB][hapmap]
rs2056417	0.83[CHB][hapmap]
rs2480784	0.84[CHB][hapmap]
rs2483677	0.83[CHB][hapmap]
rs2483686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2847336	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4285702	0.84[ASN][1000 genomes]
rs484416	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs490037	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs490960	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs515423	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs544289	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs585870	0.92[CHB][hapmap]
rs589400	0.83[CHB][hapmap]
rs596537	0.92[CHB][hapmap]
rs607941	0.92[CHB][hapmap]
rs620405	0.92[CHB][hapmap]
rs622623	0.92[CHB][hapmap]
rs647281	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs648324	0.92[CHB][hapmap]
rs648399	0.92[CHB][hapmap]
rs6540931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs660725	0.92[CHB][hapmap]
rs661256	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs661272	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662064	0.92[CHB][hapmap]
rs666103	1.00[CEU][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs668805	0.92[CHB][hapmap]
rs669701	0.92[CHB][hapmap]
rs676995	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537164	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944973	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers 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 target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer 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	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1308520	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10491400-10519000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:10491400-10521000	Weak transcription	Ovary	ovary
3	chr1:10491400-10521200	Weak transcription	Aorta	Aorta
4	chr1:10491600-10511000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:10491600-10511000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:10491600-10511200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:10491600-10516200	Weak transcription	HMEC	breast
8	chr1:10491600-10517800	Weak transcription	Primary T cells from cord blood	blood
9	chr1:10491600-10518000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:10491600-10518000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:10491600-10519200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:10491600-10521200	Weak transcription	Brain Substantia Nigra	brain
13	chr1:10491600-10521200	Weak transcription	Left Ventricle	heart
14	chr1:10491600-10521200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:10491600-10521200	Weak transcription	Spleen	Spleen
16	chr1:10491600-10521400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:10491800-10510800	Weak transcription	Osteobl	bone
18	chr1:10491800-10511000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:10491800-10511000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:10491800-10511000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:10491800-10511200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:10491800-10511400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:10491800-10511400	Weak transcription	NH-A	brain
24	chr1:10491800-10516600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:10491800-10516600	Weak transcription	HSMM	muscle
26	chr1:10491800-10520600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:10492000-10521200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:10492200-10510800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:10492400-10517200	Weak transcription	Brain Germinal Matrix	brain
30	chr1:10493200-10511400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:10493600-10516800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:10494000-10511400	Weak transcription	Stomach Mucosa	stomach
33	chr1:10494200-10518800	Weak transcription	K562	blood
34	chr1:10494200-10521400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:10495400-10519000	Weak transcription	Placenta	Placenta
36	chr1:10499200-10531400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:10499400-10519200	Weak transcription	HepG2	liver
38	chr1:10499600-10518200	Weak transcription	Primary B cells from cord blood	blood
39	chr1:10500800-10522800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:10501000-10511400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:10501200-10516200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:10501200-10519200	Weak transcription	Liver	Liver
43	chr1:10501200-10521400	Weak transcription	Brain Angular Gyrus	brain
44	chr1:10502600-10511200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:10503000-10511600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:10503400-10518000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:10503800-10518200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:10505200-10511000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:10505200-10511200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:10505200-10511400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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