Variant report

Variant	rs2238029
Chromosome Location	chr12:2218896-2218897
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	chr11:85960754..85963363-chr12:2217354..2219874,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10848617	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1558321	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1558322	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2238027	0.87[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2238033	0.91[EUR][1000 genomes]
rs2238034	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2238036	0.85[JPT][hapmap]
rs2239130	0.91[EUR][1000 genomes]
rs2239131	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239133	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2239134	0.96[EUR][1000 genomes]
rs2239135	0.89[EUR][1000 genomes]
rs2247833	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2283279	0.82[AMR][1000 genomes]
rs2283283	0.86[GIH][hapmap];0.92[MEX][hapmap]
rs2299660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299661	0.91[EUR][1000 genomes]
rs2299662	0.90[EUR][1000 genomes]
rs2299663	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2299664	1.00[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4126711	0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs4765897	0.89[EUR][1000 genomes]
rs4765898	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs6489348	0.89[GIH][hapmap];0.96[MEX][hapmap]
rs7298821	0.81[JPT][hapmap]
rs758723	0.91[EUR][1000 genomes]
rs874924	0.88[EUR][1000 genomes]
rs881303	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv521838	chr12:2060580-2299680	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1035885	chr12:2077660-2310157	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv541350	chr12:2077660-2310157	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1038722	chr12:2085035-2308205	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv541351	chr12:2085035-2308205	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv826183	chr12:2147469-2257818	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv898602	chr12:2149786-2223740	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv898603	chr12:2208390-2268143	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv998408	chr12:2212269-2219340	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1053798	chr12:2214047-2253488	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv557018	chr12:2214692-2223740	Weak transcription Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv557033	chr12:2215448-2252924	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2238029	KCNA1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2202800-2220200	Weak transcription	Fetal Brain Female	brain
2	chr12:2207200-2223000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:2208400-2226600	Weak transcription	Brain Angular Gyrus	brain
4	chr12:2211200-2221000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:2211600-2222200	Weak transcription	Spleen	Spleen
6	chr12:2211800-2229000	Weak transcription	Osteobl	bone
7	chr12:2214400-2219400	Weak transcription	Lung	lung
8	chr12:2214600-2221000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:2216800-2222600	Enhancers	Colon Smooth Muscle	Colon
10	chr12:2216800-2223600	Enhancers	Fetal Heart	heart
11	chr12:2216800-2224400	Enhancers	Left Ventricle	heart
12	chr12:2217200-2222400	Enhancers	Stomach Smooth Muscle	stomach
13	chr12:2217200-2224200	Enhancers	Right Ventricle	heart
14	chr12:2217400-2219800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:2217600-2219400	Weak transcription	Right Atrium	heart
16	chr12:2217800-2229600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:2218000-2221800	Weak transcription	Esophagus	oesophagus
18	chr12:2218200-2221200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:2218400-2219200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:2218400-2221400	Enhancers	Rectal Smooth Muscle	rectum
21	chr12:2218400-2222000	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:2218600-2219600	Weak transcription	Fetal Intestine Large	intestine
23	chr12:2218800-2219000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:2218800-2219000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:2218800-2219200	Enhancers	Aorta	Aorta

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