Variant report

Variant	rs16988244
Chromosome Location	chr22:30433373-30433374
allele	G/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:
4	chr22:30422072..30424953-chr22:30431511..30433741,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100330	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs11552852	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1544429	0.89[EUR][1000 genomes]
rs1544430	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1544431	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1544433	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16988120	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16988143	0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16988148	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16988149	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16988291	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16988303	1.00[CEU][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16988304	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16988333	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17647863	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17648208	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1807726	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2105871	0.80[EUR][1000 genomes]
rs2349228	0.85[AFR][1000 genomes]
rs2412980	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2412981	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36579	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36588	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36589	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36592	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36593	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36597	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36599	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36602	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36603	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36608	0.84[EUR][1000 genomes]
rs39713	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs41278853	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41281623	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41281633	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4482600	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4482601	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs45629133	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4820823	0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4823078	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55645000	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56392746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56406718	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57348516	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5752974	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs5752977	0.82[EUR][1000 genomes]
rs5752979	0.89[EUR][1000 genomes]
rs5753038	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753039	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753042	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753043	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763560	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs5763568	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs5763582	0.80[EUR][1000 genomes]
rs5763595	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763855	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763856	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763857	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763858	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763870	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763873	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763878	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58162368	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5997539	0.82[EUR][1000 genomes]
rs6006276	0.82[EUR][1000 genomes]
rs6006383	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60759987	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6518681	0.91[EUR][1000 genomes]
rs6519802	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6519805	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs713916	0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7284365	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7284951	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7285585	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7286205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7286441	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7287233	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7290175	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs737901	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs737938	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73883344	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73883349	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs73883354	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883355	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883358	0.82[AFR][1000 genomes]
rs73883359	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73883360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883363	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883367	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883370	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883374	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883375	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73883377	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73883378	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8141471	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs962322	0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.91[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16988244	MTMR3	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 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	chr22:30424200-30434000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr22:30424600-30435600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr22:30424800-30443000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr22:30425000-30434200	Weak transcription	Gastric	stomach
11	chr22:30425200-30434000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr22:30425200-30434200	Weak transcription	Pancreas	Pancrea
13	chr22:30425200-30434200	Weak transcription	NHLF	lung
14	chr22:30425200-30435800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr22:30425200-30438800	Weak transcription	Fetal Intestine Large	intestine
16	chr22:30425200-30440000	Weak transcription	Fetal Lung	lung
17	chr22:30425200-30440200	Weak transcription	Brain Germinal Matrix	brain
18	chr22:30425600-30439400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr22:30425800-30433800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr22:30425800-30434000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr22:30425800-30434800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr22:30425800-30435400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr22:30425800-30439800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr22:30425800-30442000	Weak transcription	Fetal Brain Female	brain
25	chr22:30426000-30434400	Weak transcription	Left Ventricle	heart
26	chr22:30426200-30434000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr22:30426200-30434200	Weak transcription	Lung	lung
28	chr22:30426600-30443000	Weak transcription	Thymus	Thymus
29	chr22:30429200-30434200	Weak transcription	Psoas Muscle	Psoas
30	chr22:30429400-30439800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr22:30429800-30434600	Weak transcription	Right Atrium	heart
32	chr22:30429800-30435000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr22:30430200-30434000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr22:30430200-30434000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr22:30430200-30442800	Weak transcription	Spleen	Spleen
36	chr22:30430200-30449600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr22:30430400-30433600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr22:30430400-30434400	Weak transcription	Liver	Liver
39	chr22:30430400-30434400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr22:30430400-30435800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr22:30430800-30436200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr22:30430800-30439400	Weak transcription	Fetal Intestine Small	intestine
43	chr22:30431600-30434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr22:30431800-30435200	Enhancers	Placenta	Placenta
45	chr22:30432400-30435000	Enhancers	Hela-S3	cervix
46	chr22:30432600-30434200	Weak transcription	Fetal Muscle Leg	muscle
47	chr22:30432800-30433800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr22:30432800-30433800	Weak transcription	NHEK	skin
49	chr22:30432800-30433800	Weak transcription	Osteobl	bone
50	chr22:30432800-30434000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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