Variant report

Variant	rs12637234
Chromosome Location	chr3:20230089-20230090
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20227831..20229515-chr3:20229924..20231692,2	MCF-7	breast:
2	chr3:20094893..20096727-chr3:20227964..20230863,2	MCF-7	breast:
3	chr3:20219250..20222131-chr3:20228592..20230370,2	K562	blood:
4	chr3:20227937..20230614-chr3:20238703..20240365,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KAT2B-1	chr3:20227726-20230848	NONHSAT088617

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11128941	0.87[EUR][1000 genomes]
rs11128942	0.87[EUR][1000 genomes]
rs1122135	0.87[EUR][1000 genomes]
rs12486706	0.87[EUR][1000 genomes]
rs1395985	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs1567200	0.85[EUR][1000 genomes]
rs17006682	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17006711	0.84[EUR][1000 genomes]
rs17006721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17006724	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17006733	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17006739	0.87[EUR][1000 genomes]
rs17797971	0.89[CEU][hapmap]
rs2068477	0.80[CEU][hapmap]
rs2292228	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3804568	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3804572	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3811674	0.81[EUR][1000 genomes]
rs3913938	0.84[EUR][1000 genomes]
rs4076369	0.87[EUR][1000 genomes]
rs41276509	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4132121	0.87[EUR][1000 genomes]
rs4858157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858159	0.85[EUR][1000 genomes]
rs4858160	0.87[EUR][1000 genomes]
rs4858770	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4858775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858776	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4858777	0.87[EUR][1000 genomes]
rs57204823	0.87[EUR][1000 genomes]
rs58206832	0.87[EUR][1000 genomes]
rs58371809	0.87[EUR][1000 genomes]
rs58409904	0.85[EUR][1000 genomes]
rs58613937	0.87[EUR][1000 genomes]
rs59189930	0.87[EUR][1000 genomes]
rs59471185	0.87[EUR][1000 genomes]
rs60612263	0.87[EUR][1000 genomes]
rs61206920	0.84[EUR][1000 genomes]
rs61207556	0.87[EUR][1000 genomes]
rs61729306	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62241665	0.81[AMR][1000 genomes]
rs62241671	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62241672	0.85[EUR][1000 genomes]
rs62241673	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62241699	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62241703	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62241706	0.89[EUR][1000 genomes]
rs62241707	0.87[EUR][1000 genomes]
rs62241708	0.89[EUR][1000 genomes]
rs62241714	0.87[EUR][1000 genomes]
rs62241752	0.87[EUR][1000 genomes]
rs62241753	0.87[EUR][1000 genomes]
rs62243138	0.82[EUR][1000 genomes]
rs62243461	0.80[EUR][1000 genomes]
rs62243480	0.85[EUR][1000 genomes]
rs62243482	0.82[EUR][1000 genomes]
rs62243502	0.82[EUR][1000 genomes]
rs62243503	0.80[EUR][1000 genomes]
rs6550401	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[EUR][1000 genomes]
rs6550413	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6550419	0.87[EUR][1000 genomes]
rs66968685	0.85[EUR][1000 genomes]
rs67253443	0.85[EUR][1000 genomes]
rs6761987	0.87[EUR][1000 genomes]
rs6767445	0.81[EUR][1000 genomes]
rs6770526	0.85[EUR][1000 genomes]
rs6774000	0.85[CEU][hapmap]
rs6774152	0.80[EUR][1000 genomes]
rs6776870	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs6777193	0.82[EUR][1000 genomes]
rs6778969	0.85[EUR][1000 genomes]
rs6782533	0.87[EUR][1000 genomes]
rs6792484	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs67949984	0.85[EUR][1000 genomes]
rs68098782	0.83[EUR][1000 genomes]
rs7620481	1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7622992	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7623136	0.82[EUR][1000 genomes]
rs7640134	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs906468	0.87[EUR][1000 genomes]
rs937886	0.87[EUR][1000 genomes]
rs9838186	0.80[EUR][1000 genomes]
rs9838851	0.85[EUR][1000 genomes]
rs9845960	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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	21 gene(s)	inside rSNPs	diseases
5	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
11	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
14	esv1832674	chr3:20152772-20605302	Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
15	esv1831853	chr3:20157077-20615273	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	esv1833208	chr3:20157077-20638228	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	esv2422249	chr3:20163608-20626956	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	esv1826144	chr3:20164282-20638228	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	nsv1013532	chr3:20172889-20305612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
20	nsv536513	chr3:20172889-20305612	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
21	esv1831289	chr3:20191506-20617984	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
22	esv1829973	chr3:20192578-20375260	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
23	esv1829847	chr3:20196923-20638228	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
24	nsv876597	chr3:20197364-20242143	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	esv1829457	chr3:20200232-20375260	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	esv1830113	chr3:20200232-20430932	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
27	esv3377463	chr3:20203472-20343029	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
28	esv3381923	chr3:20203492-20342999	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12637234	SGOL1	cis	lymphoblastoid	seeQTL
rs12637234	KAT2B	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20228400-20239400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:20228600-20231600	Weak transcription	Aorta	Aorta
3	chr3:20229000-20230600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:20229400-20238800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:20229600-20241800	Weak transcription	Ovary	ovary
6	chr3:20229800-20230200	Weak transcription	Liver	Liver

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