Variant report

Variant	rs676995
Chromosome Location	chr1:10498453-10498454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10864455	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10864456	0.87[ASN][1000 genomes]
rs1188530	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1307489	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1307490	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1307491	0.81[EUR][1000 genomes]
rs1307493	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1307494	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1307497	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1308520	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483686	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2847336	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2847337	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4285702	0.81[ASN][1000 genomes]
rs484416	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs490037	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs490960	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs515423	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs544289	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs647281	0.84[EUR][1000 genomes]
rs6540931	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs661256	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs661272	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666103	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7537164	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs944973	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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
rs676995	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10491400-10504600	Weak transcription	Lung	lung
2	chr1:10491400-10519000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:10491400-10521000	Weak transcription	Ovary	ovary
4	chr1:10491400-10521200	Weak transcription	Aorta	Aorta
5	chr1:10491600-10500000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:10491600-10500400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:10491600-10504600	Weak transcription	HSMMtube	muscle
8	chr1:10491600-10508000	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:10491600-10510200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:10491600-10510200	Weak transcription	Gastric	stomach
11	chr1:10491600-10510400	Weak transcription	Right Atrium	heart
12	chr1:10491600-10511000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:10491600-10511000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:10491600-10511200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:10491600-10516200	Weak transcription	HMEC	breast
16	chr1:10491600-10517800	Weak transcription	Primary T cells from cord blood	blood
17	chr1:10491600-10518000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:10491600-10518000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:10491600-10519200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:10491600-10521200	Weak transcription	Brain Substantia Nigra	brain
21	chr1:10491600-10521200	Weak transcription	Left Ventricle	heart
22	chr1:10491600-10521200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:10491600-10521200	Weak transcription	Spleen	Spleen
24	chr1:10491600-10521400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:10491800-10498600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:10491800-10500800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:10491800-10501000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:10491800-10504400	Weak transcription	Adipose Nuclei	Adipose
29	chr1:10491800-10504400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:10491800-10508400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:10491800-10508800	Weak transcription	Colonic Mucosa	Colon
32	chr1:10491800-10509600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:10491800-10510000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:10491800-10510200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:10491800-10510200	Weak transcription	Brain Anterior Caudate	brain
36	chr1:10491800-10510200	Weak transcription	NHLF	lung
37	chr1:10491800-10510800	Weak transcription	Osteobl	bone
38	chr1:10491800-10511000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:10491800-10511000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:10491800-10511000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:10491800-10511200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:10491800-10511400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:10491800-10511400	Weak transcription	NH-A	brain
44	chr1:10491800-10516600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:10491800-10516600	Weak transcription	HSMM	muscle
46	chr1:10491800-10520600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:10492000-10499800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:10492000-10504400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:10492000-10504400	Weak transcription	A549	lung
50	chr1:10492000-10504400	Weak transcription	NHEK	skin

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