Variant report

Variant	rs876936
Chromosome Location	chr2:47740198-47740199
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47738717..47741955-chr2:47744813..47746664,3	K562	blood:
2	chr2:47738927..47740595-chr2:47742271..47744038,2	K562	blood:
3	chr2:47738547..47740217-chr2:47745164..47747197,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNK12-2	chr2:47739991-47740615	NONHSAT070579

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10175959	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10175972	0.86[ASN][1000 genomes]
rs10188090	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10197011	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10206575	0.85[ASN][1000 genomes]
rs10206782	0.85[ASN][1000 genomes]
rs10209369	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10495945	0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11684661	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11684737	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11694689	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11886591	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11896864	0.83[AMR][1000 genomes]
rs11901645	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12712994	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12991125	0.85[ASN][1000 genomes]
rs13031342	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2059520	0.85[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs2162121	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2278139	0.82[ASN][1000 genomes]
rs2303424	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771274	0.84[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap]
rs3771276	0.82[AMR][1000 genomes]
rs3771280	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs3771281	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3821227	0.84[EUR][1000 genomes]
rs4550716	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4583514	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6544990	0.92[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6711675	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6718364	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6720555	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6724382	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6724876	0.80[AMR][1000 genomes]
rs6729015	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6744097	0.85[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6746426	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6754473	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6758327	0.82[AMR][1000 genomes]
rs6759990	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7585174	0.86[ASN][1000 genomes]
rs7586575	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7596629	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7599880	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7601062	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7606984	0.83[ASN][1000 genomes]
rs7607312	0.80[AMR][1000 genomes]
rs876937	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879722	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9784092	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	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
2	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
3	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
4	nsv998314	chr2:47720420-47959168	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv817599	chr2:47738456-47961099	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs876936	MSH2	cis	cerebellum	SCAN
rs876936	SIX2	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47732600-47747800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:47734000-47740800	Weak transcription	Brain Angular Gyrus	brain
3	chr2:47734000-47741000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:47734000-47741400	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:47734000-47747000	Weak transcription	Brain Anterior Caudate	brain
6	chr2:47734000-47747600	Weak transcription	Brain Substantia Nigra	brain
7	chr2:47736800-47742800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:47736800-47747400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:47736800-47747400	Weak transcription	Thymus	Thymus
10	chr2:47737000-47747200	Weak transcription	GM12878-XiMat	blood
11	chr2:47737200-47741200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:47737200-47741200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:47737200-47743400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:47737200-47744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:47737200-47744800	Weak transcription	Fetal Thymus	thymus
16	chr2:47738200-47742800	Weak transcription	Fetal Brain Male	brain
17	chr2:47738200-47744800	Weak transcription	Ovary	ovary
18	chr2:47738400-47743600	Weak transcription	Fetal Brain Female	brain
19	chr2:47738400-47747200	Weak transcription	Brain Germinal Matrix	brain
20	chr2:47739200-47740200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:47739200-47747600	Weak transcription	Pancreas	Pancrea
22	chr2:47739400-47740200	Enhancers	Dnd41	blood
23	chr2:47739600-47740200	Enhancers	HUVEC	blood vessel
24	chr2:47739800-47740400	Enhancers	K562	blood
25	chr2:47739800-47741600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:47740000-47740200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:47740000-47741400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:47740000-47743000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:47740000-47747200	Weak transcription	Spleen	Spleen

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