Variant report

Variant	rs3828044
Chromosome Location	chr1:10508136-10508137
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10508108-10508647	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:10507664-10508206	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10498763..10502281-chr1:10507283..10512164,5	K562	blood:

Variant related genes	Relation type
CORT	TF binding region
ENSG00000175279	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10436981	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11121572	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12126556	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12134590	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12745969	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35138970	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4846228	1.00[CHB][hapmap]
rs597441	0.82[TSI][hapmap]
rs6662684	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9970001	1.00[CHB][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3828044	PLEKHG5	cis	parietal	SCAN
rs3828044	APITD1	cis	cerebellum	SCAN
rs3828044	NPPA	cis	cerebellum	SCAN
rs3828044	ZBTB48	cis	parietal	SCAN
rs3828044	PGD	cis	Muscle Skeletal	GTEx
rs3828044	KIAA2013	cis	parietal	SCAN

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	chr1:10491600-10510200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:10491600-10510200	Weak transcription	Gastric	stomach
6	chr1:10491600-10510400	Weak transcription	Right Atrium	heart
7	chr1:10491600-10511000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:10491600-10511000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:10491600-10511200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:10491600-10516200	Weak transcription	HMEC	breast
11	chr1:10491600-10517800	Weak transcription	Primary T cells from cord blood	blood
12	chr1:10491600-10518000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:10491600-10518000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:10491600-10519200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:10491600-10521200	Weak transcription	Brain Substantia Nigra	brain
16	chr1:10491600-10521200	Weak transcription	Left Ventricle	heart
17	chr1:10491600-10521200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:10491600-10521200	Weak transcription	Spleen	Spleen
19	chr1:10491600-10521400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:10491800-10508400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:10491800-10508800	Weak transcription	Colonic Mucosa	Colon
22	chr1:10491800-10509600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:10491800-10510000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:10491800-10510200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:10491800-10510200	Weak transcription	Brain Anterior Caudate	brain
26	chr1:10491800-10510200	Weak transcription	NHLF	lung
27	chr1:10491800-10510800	Weak transcription	Osteobl	bone
28	chr1:10491800-10511000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:10491800-10511000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:10491800-10511000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:10491800-10511200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:10491800-10511400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:10491800-10511400	Weak transcription	NH-A	brain
34	chr1:10491800-10516600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:10491800-10516600	Weak transcription	HSMM	muscle
36	chr1:10491800-10520600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:10492000-10510000	Weak transcription	NHDF-Ad	bronchial
38	chr1:10492000-10521200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:10492200-10509200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:10492200-10510800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:10492400-10517200	Weak transcription	Brain Germinal Matrix	brain
42	chr1:10492800-10509400	Weak transcription	Fetal Brain Male	brain
43	chr1:10493200-10511400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:10493400-10510400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:10493600-10510200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:10493600-10516800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:10493800-10510000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:10494000-10511400	Weak transcription	Stomach Mucosa	stomach
49	chr1:10494200-10518800	Weak transcription	K562	blood
50	chr1:10494200-10521400	Weak transcription	Primary B cells from peripheral blood	blood

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