Variant report

Variant	rs42938
Chromosome Location	chr22:30965757-30965758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30964568..30966833-chr22:30970828..30972723,3	MCF-7	breast:
2	chr22:30964139..30967338-chr22:30986198..30989265,4	MCF-7	breast:
3	chr22:30964660..30967632-chr22:30970789..30972723,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100029	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16988790	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs42931	0.94[ASW][hapmap];0.92[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap]
rs42932	0.88[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs42935	0.84[EUR][1000 genomes]
rs42939	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs42941	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5997685	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv588887	chr22:30953521-30995356	Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs42938	MTMR3	cis	cerebellum	SCAN
rs42938	KIAA1671	cis	parietal	SCAN
rs42938	SLC35E4	cis	cerebellum	SCAN
rs42938	SEC14L2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30944800-30968000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:30950600-30969000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr22:30958000-30969600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr22:30960800-30969800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr22:30961000-30967200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr22:30961000-30967800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr22:30961400-30969400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr22:30961800-30968000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr22:30962200-30966200	Weak transcription	Brain Anterior Caudate	brain
10	chr22:30962200-30967000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr22:30962400-30967000	Weak transcription	Liver	Liver
12	chr22:30962600-30967200	Weak transcription	Brain Angular Gyrus	brain
13	chr22:30962600-30967800	Weak transcription	A549	lung
14	chr22:30963200-30967000	Weak transcription	Fetal Intestine Large	intestine
15	chr22:30963400-30966400	Strong transcription	Fetal Intestine Small	intestine
16	chr22:30963600-30967000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr22:30964200-30968000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr22:30964400-30970000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:30964400-30979600	Weak transcription	K562	blood
20	chr22:30964600-30966800	Weak transcription	Brain Hippocampus Middle	brain
21	chr22:30964600-30966800	Weak transcription	HepG2	liver
22	chr22:30964600-30967000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr22:30964800-30969800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr22:30965400-30965800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
25	chr22:30965400-30966200	Enhancers	Brain Cingulate Gyrus	brain
26	chr22:30965400-30966200	Enhancers	Brain Substantia Nigra	brain
27	chr22:30965400-30969000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr22:30965600-30965800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr22:30965600-30965800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr22:30965600-30968400	Weak transcription	Gastric	stomach
31	chr22:30965600-30971000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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