Variant report

Variant	rs6720549
Chromosome Location	chr2:47714419-47714420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNK12-1	chr2:47713153-47714936	ENSG00000236558.2

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10175959	0.81[ASN][1000 genomes]
rs10175972	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10179452	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10185866	0.91[CEU][hapmap]
rs10188090	0.82[ASN][1000 genomes]
rs10206575	0.90[EUR][1000 genomes]
rs10206782	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10209369	0.82[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11684661	0.82[ASN][1000 genomes]
rs11684737	0.82[ASN][1000 genomes]
rs11886591	0.83[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12991125	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13031342	0.88[EUR][1000 genomes]
rs1981928	0.91[EUR][1000 genomes]
rs2059520	0.83[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]
rs3732182	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3732183	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3764959	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3764960	0.82[ASN][1000 genomes]
rs3771274	0.80[JPT][hapmap]
rs3771278	0.81[ASN][1000 genomes]
rs3771279	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3771280	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821227	0.82[ASN][1000 genomes]
rs4550716	0.81[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4583514	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6544992	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6711675	0.82[JPT][hapmap]
rs6720555	0.95[ASN][1000 genomes]
rs6725042	0.87[EUR][1000 genomes]
rs6726691	0.90[EUR][1000 genomes]
rs6737303	0.92[EUR][1000 genomes]
rs6748435	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6757035	0.91[EUR][1000 genomes]
rs6759990	0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7584256	0.91[CEU][hapmap]
rs7585174	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7588420	0.82[EUR][1000 genomes]
rs7596629	0.80[ASN][1000 genomes]
rs7607076	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6720549	MSH2	cis	Artery Tibial	GTEx
rs6720549	MSH2	cis	lung	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47658200-47714800	Weak transcription	HSMMtube	muscle
2	chr2:47658200-47724800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:47658400-47716000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:47685000-47715000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:47691600-47715400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:47691600-47715600	Weak transcription	NHEK	skin
7	chr2:47691600-47716000	Weak transcription	Gastric	stomach
8	chr2:47691600-47716000	Weak transcription	Pancreas	Pancrea
9	chr2:47693600-47715400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:47693600-47716800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:47694200-47715600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:47696000-47716000	Weak transcription	NHLF	lung
13	chr2:47696800-47716000	Weak transcription	Lung	lung
14	chr2:47697000-47716200	Weak transcription	Fetal Brain Female	brain
15	chr2:47697200-47715400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:47697600-47715600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:47700400-47714800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:47702800-47727000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:47703800-47716000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:47703800-47722000	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:47704200-47716200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:47705800-47717000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:47706000-47715800	Weak transcription	HUVEC	blood vessel
24	chr2:47706000-47715800	Weak transcription	NH-A	brain
25	chr2:47706200-47716200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:47706600-47716200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:47708400-47716000	Weak transcription	HSMM	muscle
28	chr2:47710000-47716200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:47712000-47715400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:47712000-47716000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:47712000-47716000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:47712000-47716200	Weak transcription	Fetal Stomach	stomach
33	chr2:47712200-47715600	Weak transcription	HMEC	breast
34	chr2:47712200-47716400	Weak transcription	Fetal Intestine Large	intestine
35	chr2:47712200-47716400	Weak transcription	Left Ventricle	heart
36	chr2:47712600-47715600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:47712600-47716000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:47712600-47716000	Weak transcription	Fetal Thymus	thymus
39	chr2:47712600-47716000	Weak transcription	Thymus	Thymus
40	chr2:47712600-47716400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:47712600-47716400	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:47712600-47716600	Weak transcription	HepG2	liver
43	chr2:47712800-47714600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr2:47712800-47715600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:47712800-47716200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:47712800-47716400	Weak transcription	Hela-S3	cervix
47	chr2:47712800-47721800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr2:47713000-47716200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:47713000-47716200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:47713000-47716400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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