Variant report

Variant	rs1191774
Chromosome Location	chr2:20139224-20139225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20138877..20140913-chr2:20142589..20144773,2	MCF-7	breast:
2	chr2:20138433..20141277-chr2:20142757..20144627,2	K562	blood:
3	chr2:20131153..20134079-chr2:20137920..20140711,2	MCF-7	breast:
4	chr2:20101371..20103225-chr2:20137366..20140099,2	K562	blood:

Variant related genes	Relation type
ENSG00000271991	Chromatin interaction
ENSG00000183891	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10153717	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10856791	0.81[ASN][1000 genomes]
rs1119094	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11694716	0.84[ASN][1000 genomes]
rs1191776	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1191778	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1191803	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1437862	0.81[ASN][1000 genomes]
rs1816647	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2028206	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2028207	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118444	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278525	0.81[ASN][1000 genomes]
rs4035118	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6718556	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7574119	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
3	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv527453	chr2:20109061-20160209	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1798392	chr2:20131079-20173255	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1191774	MATN3	cis	Artery Tibial	GTEx
rs1191774	MATN3	cis	Esophagus Muscularis	GTEx
rs1191774	MATN3	cis	Artery Aorta	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
2	chr2:20114400-20143800	Weak transcription	Brain Substantia Nigra	brain
3	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:20124800-20142800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:20127400-20167800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
8	chr2:20129400-20143000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:20129400-20144000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
11	chr2:20129600-20149800	Weak transcription	Spleen	Spleen
12	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:20130400-20140200	Weak transcription	Liver	Liver
15	chr2:20130400-20141800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:20130400-20142000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:20130400-20142600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:20130400-20149400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:20130400-20149400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:20130400-20164600	Weak transcription	Lung	lung
21	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:20130600-20139800	Weak transcription	Fetal Stomach	stomach
23	chr2:20130600-20140000	Weak transcription	K562	blood
24	chr2:20130600-20142800	Weak transcription	Fetal Intestine Small	intestine
25	chr2:20130600-20143800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:20130600-20161200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:20133600-20140800	Weak transcription	Hela-S3	cervix
30	chr2:20133600-20164800	Weak transcription	Gastric	stomach
31	chr2:20133600-20184800	Weak transcription	Psoas Muscle	Psoas
32	chr2:20133800-20151600	Weak transcription	Fetal Kidney	kidney
33	chr2:20133800-20173200	Weak transcription	NHEK	skin
34	chr2:20133800-20176800	Weak transcription	HMEC	breast
35	chr2:20134200-20168600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:20134400-20146800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:20134600-20148400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:20135800-20141600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:20136400-20148800	Weak transcription	HSMM	muscle
40	chr2:20136400-20150800	Weak transcription	Thymus	Thymus
41	chr2:20136400-20177000	Weak transcription	GM12878-XiMat	blood
42	chr2:20136400-20177200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:20136600-20141800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:20136600-20144200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:20136600-20149400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:20136600-20151600	Weak transcription	Brain Germinal Matrix	brain
47	chr2:20136600-20171200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:20136600-20177200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:20136800-20139800	Weak transcription	Ovary	ovary
50	chr2:20136800-20171400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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