Variant report

Variant	rs498033
Chromosome Location	chr3:156034741-156034742
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1375926	0.91[GIH][hapmap]
rs4056367	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv877682	chr3:156019961-156077514	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs498033	SLC33A1	cis	cerebellum	SCAN
rs498033	SHOX2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156021400-156035200	Weak transcription	Stomach Mucosa	stomach
2	chr3:156021800-156035800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:156022800-156035600	Weak transcription	Brain Anterior Caudate	brain
4	chr3:156026400-156038400	Weak transcription	Aorta	Aorta
5	chr3:156029800-156035000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:156030000-156035000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:156030000-156035200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:156030000-156035400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:156030000-156035400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:156030000-156035400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:156030200-156034800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:156030600-156036400	Enhancers	Hela-S3	cervix
13	chr3:156030800-156035600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:156032000-156035000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:156032000-156035200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:156033200-156037000	Weak transcription	Left Ventricle	heart
17	chr3:156034000-156036000	Enhancers	Rectal Smooth Muscle	rectum
18	chr3:156034000-156036600	Enhancers	HUVEC	blood vessel
19	chr3:156034400-156035000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:156034400-156035800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:156034400-156036000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:156034400-156036200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:156034400-156036200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:156034400-156036400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:156034600-156036400	Enhancers	HMEC	breast
26	chr3:156034600-156036400	Enhancers	NHEK	skin

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