Variant report

Variant	rs12198920
Chromosome Location	chr6:71307347-71307348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 141 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10485118	0.86[JPT][hapmap]
rs10485119	0.86[JPT][hapmap]
rs1075262	0.92[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs1075263	0.86[JPT][hapmap]
rs10945230	0.86[JPT][hapmap]
rs10945236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1140297	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11965656	0.86[JPT][hapmap]
rs1208476	0.91[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1208477	0.92[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs12190556	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12197942	0.86[JPT][hapmap]
rs12197963	0.86[JPT][hapmap]
rs12203298	0.86[JPT][hapmap]
rs12205103	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209965	0.86[JPT][hapmap]
rs12215765	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12216376	0.86[JPT][hapmap]
rs12526164	0.86[JPT][hapmap]
rs12526827	0.86[JPT][hapmap]
rs12527634	0.86[JPT][hapmap]
rs12529284	0.86[JPT][hapmap]
rs13199529	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13206086	0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13213357	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13437371	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13654	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534050	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16869156	0.92[JPT][hapmap]
rs16869158	0.92[JPT][hapmap]
rs16869170	0.86[JPT][hapmap]
rs16869221	0.86[JPT][hapmap]
rs16869228	0.84[JPT][hapmap]
rs16869238	0.86[JPT][hapmap]
rs16869243	0.86[JPT][hapmap]
rs16869267	0.86[JPT][hapmap]
rs16869273	0.86[JPT][hapmap]
rs16869338	0.86[JPT][hapmap]
rs16869353	0.86[JPT][hapmap]
rs16869370	0.86[JPT][hapmap]
rs16869371	0.86[JPT][hapmap]
rs16869373	0.85[JPT][hapmap]
rs16880770	0.86[JPT][hapmap]
rs1739338	0.86[JPT][hapmap]
rs1917344	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2207423	0.86[JPT][hapmap]
rs2273210	0.86[JPT][hapmap]
rs2293297	0.86[JPT][hapmap]
rs2295200	0.86[JPT][hapmap]
rs2346889	0.86[JPT][hapmap]
rs2346890	0.86[JPT][hapmap]
rs2347427	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2639297	0.86[JPT][hapmap]
rs2691505	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691506	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2747702	0.86[JPT][hapmap]
rs2747703	0.92[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs3193656	0.84[JPT][hapmap]
rs34378057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34873840	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35516318	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35542509	0.84[ASN][1000 genomes]
rs3736751	0.86[JPT][hapmap]
rs3763251	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846750	0.86[JPT][hapmap]
rs3889007	0.86[JPT][hapmap]
rs4283855	0.86[JPT][hapmap]
rs4496758	0.86[JPT][hapmap]
rs6455370	0.86[JPT][hapmap]
rs6455371	0.82[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6900840	0.84[JPT][hapmap]
rs6902797	0.82[JPT][hapmap]
rs6906572	0.86[JPT][hapmap]
rs6906592	0.86[JPT][hapmap]
rs6910903	0.86[JPT][hapmap]
rs6911812	0.85[JPT][hapmap]
rs6911983	0.86[JPT][hapmap]
rs6913548	0.85[JPT][hapmap]
rs6916974	0.86[JPT][hapmap]
rs6917368	0.86[JPT][hapmap]
rs6922680	0.86[JPT][hapmap]
rs6925112	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925839	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926591	0.86[JPT][hapmap]
rs6930397	0.86[JPT][hapmap]
rs6933150	0.86[JPT][hapmap]
rs6933784	0.86[JPT][hapmap]
rs6939478	0.86[JPT][hapmap]
rs6939814	0.86[JPT][hapmap]
rs6940416	0.92[JPT][hapmap]
rs6942012	0.86[JPT][hapmap]
rs7341224	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7739098	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7740873	0.86[JPT][hapmap]
rs7741265	0.86[JPT][hapmap]
rs7752409	0.86[JPT][hapmap]
rs7753355	0.86[JPT][hapmap]
rs7756652	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7757026	0.86[JPT][hapmap]
rs7759464	0.86[JPT][hapmap]
rs7765110	0.86[JPT][hapmap]
rs7766075	0.86[JPT][hapmap]
rs7767109	0.86[JPT][hapmap]
rs7769582	0.86[JPT][hapmap]
rs7775962	0.86[JPT][hapmap]
rs9283835	0.86[JPT][hapmap]
rs9294868	0.86[JPT][hapmap]
rs9294872	0.86[JPT][hapmap]
rs9294874	0.86[JPT][hapmap]
rs9294876	0.86[JPT][hapmap]
rs9446245	0.86[JPT][hapmap]
rs9446248	0.81[JPT][hapmap]
rs9446267	0.86[JPT][hapmap]
rs9446271	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9446272	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9446273	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9446274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9455092	0.86[JPT][hapmap]
rs9455104	0.86[JPT][hapmap]
rs9455113	0.86[JPT][hapmap]
rs9455121	0.86[JPT][hapmap]
rs9455130	0.86[JPT][hapmap]
rs9455132	0.86[JPT][hapmap]
rs9455133	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9455160	0.86[JPT][hapmap]
rs9455162	0.86[JPT][hapmap]
rs9455163	0.86[JPT][hapmap]
rs9455173	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9455179	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9455180	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9455185	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9455186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs998986	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv886145	chr6:71119524-71317480	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv886146	chr6:71219464-71317480	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12198920	C6orf57	cis	lung	GTEx
rs12198920	C6orf57	cis	cerebellum	SCAN
rs12198920	C6orf57	cis	Thyroid	GTEx
rs12198920	C6orf57	cis	parietal	SCAN
rs12198920	C6orf57	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71277200-71310600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:71278200-71308800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:71278600-71308800	Weak transcription	Dnd41	blood
4	chr6:71286200-71310600	Weak transcription	Right Ventricle	heart
5	chr6:71288400-71309800	Weak transcription	Spleen	Spleen
6	chr6:71289800-71310200	Weak transcription	Colonic Mucosa	Colon
7	chr6:71291400-71307800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:71291600-71310000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:71292600-71310000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:71295400-71308800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:71295400-71314000	Weak transcription	Aorta	Aorta
12	chr6:71295800-71309000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr6:71296200-71310600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:71298000-71310800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:71300800-71310200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:71301000-71309600	Weak transcription	Ovary	ovary
17	chr6:71301000-71310000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:71301200-71308800	Weak transcription	Primary T cells from cord blood	blood
19	chr6:71301200-71309800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:71303000-71308800	Weak transcription	Fetal Stomach	stomach

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