Variant report

Variant	rs6494127
Chromosome Location	chr15:59923085-59923086
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59922295..59925981-chr15:59927232..59929726,3	K562	blood:

Extended variants
information (count: 119 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1002181	0.80[EUR][1000 genomes]
rs10152209	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10152414	0.84[EUR][1000 genomes]
rs10152415	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs10152509	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10162629	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1046053	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1057059	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11071465	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11071468	0.81[EUR][1000 genomes]
rs11071469	0.81[EUR][1000 genomes]
rs1135148	0.86[CEU][hapmap];0.93[TSI][hapmap]
rs11634067	0.83[EUR][1000 genomes]
rs11637071	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11637359	0.91[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11853610	0.82[EUR][1000 genomes]
rs11853644	0.86[ASN][1000 genomes]
rs11854063	0.91[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs12441240	0.84[EUR][1000 genomes]
rs12593480	0.81[EUR][1000 genomes]
rs12708458	0.83[EUR][1000 genomes]
rs12708459	0.84[EUR][1000 genomes]
rs12902582	0.91[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs12902774	0.87[EUR][1000 genomes]
rs12906392	0.83[EUR][1000 genomes]
rs12907641	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12909005	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12910751	0.84[EUR][1000 genomes]
rs12912652	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1531638	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1531639	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1552031	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs1871499	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1871500	0.91[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs1871503	0.90[EUR][1000 genomes]
rs1871504	0.88[CHB][hapmap]
rs1979422	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2101019	0.95[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2170062	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306354	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs2306355	0.91[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2307273	0.89[ASW][hapmap];0.91[CEU][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2307275	0.82[ASW][hapmap];0.91[CEU][hapmap];0.93[TSI][hapmap]
rs2414638	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28671744	0.83[EUR][1000 genomes]
rs2899649	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34797071	0.83[EUR][1000 genomes]
rs34894301	0.82[EUR][1000 genomes]
rs3825870	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs4232	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs4270113	0.83[ASW][hapmap];0.91[CEU][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4774340	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs4774341	0.84[EUR][1000 genomes]
rs4775191	0.85[EUR][1000 genomes]
rs4775195	0.91[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4775197	0.91[CEU][hapmap]
rs6151458	0.90[CEU][hapmap]
rs6151461	0.91[CEU][hapmap];0.93[TSI][hapmap]
rs6151462	0.91[CEU][hapmap];0.90[TSI][hapmap]
rs6151483	0.82[ASW][hapmap];0.91[CEU][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs6151487	0.89[EUR][1000 genomes]
rs6151503	0.80[EUR][1000 genomes]
rs6151504	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs6151506	0.80[EUR][1000 genomes]
rs6151510	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6151514	0.86[CEU][hapmap]
rs6151525	0.91[CEU][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151529	0.89[CEU][hapmap]
rs6151532	0.91[CEU][hapmap]
rs6151533	0.91[CEU][hapmap]
rs6151535	0.86[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6151536	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs6151542	0.81[EUR][1000 genomes]
rs6151545	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6151551	0.91[CEU][hapmap];0.80[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151553	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151557	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6151561	0.91[CEU][hapmap];0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151565	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151568	0.91[CEU][hapmap];0.90[TSI][hapmap]
rs6151570	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151571	0.91[CEU][hapmap]
rs6151576	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151580	0.84[EUR][1000 genomes]
rs6151586	0.91[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs6151588	0.82[ASW][hapmap];0.91[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs6151589	0.91[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6151590	0.82[EUR][1000 genomes]
rs6151592	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62012358	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62014429	0.86[ASN][1000 genomes]
rs62015260	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62015289	0.81[EUR][1000 genomes]
rs6494128	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6494130	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6494131	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs6494133	0.82[EUR][1000 genomes]
rs67697180	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67820349	0.80[EUR][1000 genomes]
rs7162964	0.85[CEU][hapmap]
rs7164756	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs7172270	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7178050	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7180408	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs7182962	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7497974	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7882	0.83[ASW][hapmap];0.91[CEU][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8025415	0.83[ASW][hapmap]
rs8027679	0.82[EUR][1000 genomes]
rs8033161	0.82[EUR][1000 genomes]
rs8035465	0.85[EUR][1000 genomes]
rs8040114	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8041394	0.95[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats 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
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6494127	GTF2A2	cis	parietal	SCAN
rs6494127	PRTG	cis	parietal	SCAN
rs6494127	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59905200-59931600	Weak transcription	Fetal Stomach	stomach
2	chr15:59905200-59946200	Weak transcription	Gastric	stomach
3	chr15:59909000-59930200	Weak transcription	Fetal Intestine Large	intestine
4	chr15:59911400-59929800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:59912000-59932600	Weak transcription	Colonic Mucosa	Colon
6	chr15:59912200-59928400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:59912200-59935000	Weak transcription	Fetal Intestine Small	intestine
8	chr15:59914800-59937800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:59917800-59927800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:59917800-59930200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:59919800-59928200	Weak transcription	HSMMtube	muscle
12	chr15:59920600-59928600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:59920600-59947000	Weak transcription	Small Intestine	intestine
14	chr15:59922200-59929800	Weak transcription	GM12878-XiMat	blood
15	chr15:59922600-59928000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:59922800-59924800	Weak transcription	A549	lung
17	chr15:59922800-59925000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:59923000-59930200	Weak transcription	Osteobl	bone

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