Variant report

Variant	rs5763918
Chromosome Location	chr22:30661184-30661185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30658496..30661192-chr22:30669328..30671945,2	K562	blood:
2	chr22:30658407..30662211-chr22:30782039..30784785,6	MCF-7	breast:
3	chr22:30660277..30662001-chr22:30780639..30782477,2	MCF-7	breast:
4	chr22:30660837..30662614-chr22:30683520..30685637,2	MCF-7	breast:
5	chr22:30658735..30661229-chr22:30678360..30682105,3	MCF-7	breast:
6	chr22:30659097..30662032-chr22:30782521..30784593,3	MCF-7	breast:
7	chr22:30658717..30661351-chr22:30661980..30663935,2	K562	blood:

Variant related genes	Relation type
ENSG00000099985	Chromatin interaction
ENSG00000239282	Chromatin interaction
ENSG00000099999	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2070889	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6006421	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7289095	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[LWK][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	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
3	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv914969	chr22:30619599-30691631	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv914971	chr22:30640308-30691631	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv914972	chr22:30640308-30693581	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	esv1799458	chr22:30659798-30698035	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv588885	chr22:30661184-30691631	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5763918	MTMR3	cis	parietal	SCAN
rs5763918	SLC5A1	cis	cerebellum	SCAN
rs5763918	THOC5	cis	parietal	SCAN
rs5763918	SMTN	cis	cerebellum	SCAN
rs5763918	TPST2	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30650000-30661400	Weak transcription	GM12878-XiMat	blood
2	chr22:30654600-30661600	Weak transcription	Thymus	Thymus
3	chr22:30656200-30662000	Enhancers	Primary hematopoietic stem cells	blood
4	chr22:30656800-30661800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr22:30658200-30661400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr22:30658200-30665200	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr22:30658400-30661400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr22:30658400-30661400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr22:30659200-30661200	Weak transcription	Primary T cells from cord blood	blood
10	chr22:30659200-30661400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
11	chr22:30659400-30661200	Enhancers	Primary B cells from cord blood	blood
12	chr22:30659400-30661400	Weak transcription	K562	blood
13	chr22:30659400-30661600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr22:30659400-30661600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr22:30659400-30661800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr22:30659400-30662000	Weak transcription	Liver	Liver
17	chr22:30659400-30662000	Weak transcription	Brain Anterior Caudate	brain
18	chr22:30659400-30662000	Weak transcription	Brain Hippocampus Middle	brain
19	chr22:30659400-30662000	Weak transcription	Fetal Intestine Large	intestine
20	chr22:30659400-30662200	Weak transcription	Brain Substantia Nigra	brain
21	chr22:30659400-30662600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr22:30659400-30663200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr22:30659600-30661200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr22:30659600-30661200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr22:30659600-30661200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr22:30659600-30661400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr22:30659600-30661400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr22:30659600-30661400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr22:30659600-30661800	Weak transcription	Colonic Mucosa	Colon
30	chr22:30659600-30661800	Weak transcription	Esophagus	oesophagus
31	chr22:30659600-30662000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr22:30659600-30662000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr22:30659600-30662200	Weak transcription	Pancreas	Pancrea
34	chr22:30659600-30663000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr22:30659600-30673000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr22:30659800-30661200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
37	chr22:30659800-30661200	Weak transcription	Placenta	Placenta
38	chr22:30659800-30661400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr22:30659800-30661600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr22:30659800-30662000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr22:30659800-30662400	Weak transcription	Fetal Intestine Small	intestine
42	chr22:30660000-30661200	Weak transcription	A549	lung
43	chr22:30660000-30662000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr22:30660400-30661200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr22:30660400-30661400	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr22:30660600-30661400	Enhancers	Primary T cells fromperipheralblood	blood
47	chr22:30660600-30661600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr22:30660600-30661600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr22:30660600-30661800	Weak transcription	Gastric	stomach
50	chr22:30660800-30661200	Enhancers	Monocytes-CD14+_RO01746	blood

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