Variant report

Variant	rs16987156
Chromosome Location	chr22:30434123-30434124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30417458..30419052-chr22:30433262..30435656,2	K562	blood:
2	chr22:30431981..30436228-chr22:30436988..30442132,5	MCF-7	breast:
3	chr22:30426124..30429580-chr22:30433201..30436027,3	K562	blood:

Variant related genes	Relation type
ENSG00000100330	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11913168	0.83[CHB][hapmap]
rs12373962	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12484336	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16988084	0.94[AMR][1000 genomes]
rs16988135	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16988383	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs28428766	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28522206	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28595572	0.92[AMR][1000 genomes]
rs3788421	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57462999	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57653653	0.94[AMR][1000 genomes]
rs61352751	0.94[AMR][1000 genomes]
rs7284538	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7285751	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7286551	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7286905	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7290085	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7292732	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73161099	0.94[AMR][1000 genomes]
rs73162731	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73162773	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73164739	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73883345	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8138677	0.94[AMR][1000 genomes]
rs8139217	0.82[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8140366	0.88[AMR][1000 genomes]
rs8140770	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9306466	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9608822	0.94[AMR][1000 genomes]
rs9608823	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9608836	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608843	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9608845	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9608847	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9614071	0.85[AMR][1000 genomes]
rs9614075	0.90[AMR][1000 genomes]
rs9614083	0.94[AMR][1000 genomes]
rs9614087	0.94[AMR][1000 genomes]
rs9614089	0.94[AMR][1000 genomes]
rs9614097	0.94[AMR][1000 genomes]
rs9614101	0.90[AMR][1000 genomes]
rs9614105	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9614108	0.94[AMR][1000 genomes]
rs9614109	0.88[AMR][1000 genomes]
rs9614110	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9614111	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9614122	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9614124	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9614127	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9614128	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9614129	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9614131	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9614132	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9614143	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9614144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9614145	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9614152	0.82[EUR][1000 genomes]
rs9614153	0.82[EUR][1000 genomes]
rs9680595	0.98[AMR][1000 genomes]
rs9680809	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9983	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS 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 miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs16987156	MTMR3	cis	parietal	SCAN
rs16987156	MTMR3	cis	Nerve Tibial	GTEx
rs16987156	MTMR3	cis	Artery Aorta	GTEx
rs16987156	MTMR3	cis	lung	GTEx
rs16987156	MTMR3	cis	Artery Tibial	GTEx
rs16987156	MTMR3	cis	Adipose Subcutaneous	GTEx
rs16987156	CRYBB2P1	cis	cerebellum	SCAN
rs16987156	MTMR3	cis	Thyroid	GTEx
rs16987156	MTMR3	cis	multi-tissue	Pritchard
rs16987156	INPP5J	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30419600-30434400	Weak transcription	Small Intestine	intestine
3	chr22:30422400-30434200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr22:30422400-30434200	Weak transcription	HUVEC	blood vessel
5	chr22:30423400-30434400	Weak transcription	A549	lung
6	chr22:30423600-30447600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr22:30424600-30435600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr22:30424800-30443000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr22:30425000-30434200	Weak transcription	Gastric	stomach
10	chr22:30425200-30434200	Weak transcription	Pancreas	Pancrea
11	chr22:30425200-30434200	Weak transcription	NHLF	lung
12	chr22:30425200-30435800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr22:30425200-30438800	Weak transcription	Fetal Intestine Large	intestine
14	chr22:30425200-30440000	Weak transcription	Fetal Lung	lung
15	chr22:30425200-30440200	Weak transcription	Brain Germinal Matrix	brain
16	chr22:30425600-30439400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr22:30425800-30434800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr22:30425800-30435400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr22:30425800-30439800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr22:30425800-30442000	Weak transcription	Fetal Brain Female	brain
21	chr22:30426000-30434400	Weak transcription	Left Ventricle	heart
22	chr22:30426200-30434200	Weak transcription	Lung	lung
23	chr22:30426600-30443000	Weak transcription	Thymus	Thymus
24	chr22:30429200-30434200	Weak transcription	Psoas Muscle	Psoas
25	chr22:30429400-30439800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr22:30429800-30434600	Weak transcription	Right Atrium	heart
27	chr22:30429800-30435000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr22:30430200-30442800	Weak transcription	Spleen	Spleen
29	chr22:30430200-30449600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr22:30430400-30434400	Weak transcription	Liver	Liver
31	chr22:30430400-30434400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr22:30430400-30435800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr22:30430800-30436200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr22:30430800-30439400	Weak transcription	Fetal Intestine Small	intestine
35	chr22:30431800-30435200	Enhancers	Placenta	Placenta
36	chr22:30432400-30435000	Enhancers	Hela-S3	cervix
37	chr22:30432600-30434200	Weak transcription	Fetal Muscle Leg	muscle
38	chr22:30432800-30434200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr22:30432800-30434200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr22:30432800-30434200	Weak transcription	Esophagus	oesophagus
41	chr22:30432800-30434200	Weak transcription	Stomach Mucosa	stomach
42	chr22:30432800-30434200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr22:30432800-30434400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr22:30432800-30438800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr22:30432800-30439600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr22:30432800-30439800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr22:30432800-30440800	Weak transcription	Fetal Stomach	stomach
48	chr22:30433000-30434600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr22:30433000-30436200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr22:30433600-30435000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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