Variant report

Variant	rs7529874
Chromosome Location	chr1:169851159-169851160
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169847146..169850317-chr1:169850331..169854277,4	K562	blood:
2	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10753798	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800478	0.91[EUR][1000 genomes]
rs6704382	0.90[EUR][1000 genomes]
rs9803717	0.93[EUR][1000 genomes]
rs9803860	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7529874	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs7529874	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
3	chr1:169833800-169860200	Weak transcription	HMEC	breast
4	chr1:169842200-169857400	Weak transcription	Fetal Brain Male	brain
5	chr1:169842400-169855600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:169842400-169860000	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:169842600-169854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:169843600-169855000	Weak transcription	NHEK	skin
9	chr1:169844000-169851200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:169844000-169851200	Weak transcription	Pancreas	Pancrea
11	chr1:169844000-169860000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:169844400-169857400	Weak transcription	K562	blood
13	chr1:169844800-169851200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:169844800-169854600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:169844800-169855400	Weak transcription	Hela-S3	cervix
16	chr1:169844800-169856000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:169844800-169860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:169845000-169854000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:169845200-169853800	Weak transcription	Fetal Kidney	kidney
20	chr1:169845200-169854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:169845200-169855000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:169845200-169857200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:169845200-169857200	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:169845200-169857400	Weak transcription	HUVEC	blood vessel
25	chr1:169845200-169861400	Weak transcription	Right Ventricle	heart
26	chr1:169845200-169861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:169845400-169853400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:169845400-169859600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:169845400-169860000	Weak transcription	Psoas Muscle	Psoas
30	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:169845600-169855000	Weak transcription	Fetal Brain Female	brain
32	chr1:169845800-169855600	Weak transcription	A549	lung
33	chr1:169846000-169854600	Weak transcription	HSMMtube	muscle
34	chr1:169846000-169858000	Weak transcription	Small Intestine	intestine
35	chr1:169847000-169852000	Weak transcription	Ovary	ovary
36	chr1:169847000-169859000	Weak transcription	Left Ventricle	heart
37	chr1:169847200-169855600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:169847200-169860000	Weak transcription	Brain Substantia Nigra	brain
39	chr1:169847200-169860000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:169847400-169854600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:169847400-169855000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:169847400-169860000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:169847600-169853600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:169847600-169855000	Weak transcription	NHLF	lung
45	chr1:169847600-169855200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:169847800-169851800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:169847800-169854000	Weak transcription	NHDF-Ad	bronchial
48	chr1:169847800-169854200	Weak transcription	HSMM	muscle
49	chr1:169848000-169854400	Weak transcription	Brain Anterior Caudate	brain
50	chr1:169848000-169855600	Weak transcription	NH-A	brain

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