Variant report

Variant	rs841928
Chromosome Location	chr5:101627435-101627436
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:101626744..101629663-chr5:101630622..101633299,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173930	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10038809	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10041507	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10041525	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10041806	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10051525	0.85[ASN][1000 genomes]
rs10053573	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10055023	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs10057529	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057599	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062613	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10065821	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10069193	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs10069466	0.89[ASN][1000 genomes]
rs10073052	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10223273	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10479191	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479216	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1078338	0.82[ASN][1000 genomes]
rs1118008	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11746217	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs1376894	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs1376898	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs1376910	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs1376911	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1452057	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1452059	0.91[ASN][1000 genomes]
rs1452060	0.82[ASN][1000 genomes]
rs1542296	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs1545487	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs1545488	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs1562960	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs1562961	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1597771	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs17273466	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs1823694	0.82[ASN][1000 genomes]
rs1875634	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs1901512	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1901520	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1901521	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs1901522	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2004550	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004551	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010590	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060833	0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2084826	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2123133	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs2123135	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2400795	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs2400796	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs2400797	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2400798	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs2400801	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2548726	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2600831	0.83[JPT][hapmap]
rs28532891	0.82[ASN][1000 genomes]
rs2895806	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3114660	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3114661	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs4085107	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4343814	0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703226	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4703230	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4703232	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs56881277	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62372208	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62372209	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62372210	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6596482	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs6596493	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6596495	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6866255	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6871070	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6871966	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6873305	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6873738	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6877722	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6878190	0.91[ASN][1000 genomes]
rs6881331	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882313	0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884162	0.82[ASN][1000 genomes]
rs6885800	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6890130	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6893723	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6895200	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6895407	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs709371	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709372	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7356647	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7701832	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702418	0.82[ASN][1000 genomes]
rs7710414	0.95[YRI][hapmap]
rs7711687	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7715217	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7719316	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7721084	0.95[CHB][hapmap]
rs7721548	0.82[ASN][1000 genomes]
rs7722680	0.82[ASN][1000 genomes]
rs7731256	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7731310	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7732942	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7733253	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7734926	0.87[ASN][1000 genomes]
rs7736579	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7737204	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs841921	0.91[ASN][1000 genomes]
rs841923	0.91[ASN][1000 genomes]
rs841924	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs841925	0.91[ASN][1000 genomes]
rs841926	0.85[AFR][1000 genomes]
rs841927	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs841929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs841930	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs841931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs841933	0.83[JPT][hapmap]
rs896544	0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896545	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285943	1.00[CHB][hapmap]
rs9327859	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs9327860	1.00[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022551	chr5:101366177-101649643	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv882505	chr5:101397849-101652251	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1028787	chr5:101432086-101718569	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817537	chr5:101489151-101992104	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1016176	chr5:101534391-102333606	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv537831	chr5:101534391-102333606	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised 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	24 gene(s)	inside rSNPs	diseases
7	nsv522882	chr5:101596633-101782930	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1029894	chr5:101620079-102516827	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs841928	SLCO4C1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:101613400-101629400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:101619200-101630800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:101620600-101630600	Weak transcription	GM12878-XiMat	blood
4	chr5:101622800-101630200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:101624400-101631400	Weak transcription	Pancreas	Pancrea
6	chr5:101625200-101629000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:101625400-101630600	Weak transcription	Liver	Liver
8	chr5:101626000-101630000	Weak transcription	Fetal Intestine Small	intestine
9	chr5:101626200-101629000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:101626200-101629400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:101627200-101628800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr5:101627200-101630400	Weak transcription	HepG2	liver
13	chr5:101627400-101627600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:101627400-101629400	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr5:101627400-101630200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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