Variant report

Variant	rs4933194
Chromosome Location	chr10:92511367-92511368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:92510841..92511818-chr10:92622320..92623307,5	MCF-7	breast:
2	chr10:92511236..92511850-chr10:92630669..92631482,2	K562	blood:
3	chr10:92510928..92512332-chr10:92630672..92631466,5	MCF-7	breast:
4	chr10:92510777..92511813-chr10:92622355..92623374,9	MCF-7	breast:
5	chr10:92510876..92511819-chr10:92622380..92623098,6	K562	blood:
6	chr10:92510904..92511887-chr10:92547546..92548208,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148688	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10509613	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs10881832	0.83[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10881836	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10881847	0.85[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs10881849	0.81[EUR][1000 genomes]
rs11186297	0.92[CEU][hapmap];0.89[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11186300	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11186342	0.84[EUR][1000 genomes]
rs1274443	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1274445	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1274446	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1274447	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1274448	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1342085	0.82[ASN][1000 genomes]
rs1418212	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1935347	0.92[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1954505	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2420367	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2795317	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2800145	0.92[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2800146	0.92[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3939	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs4113478	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4471341	0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6583735	0.83[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6583736	0.83[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7073423	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7082558	0.88[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7101168	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7900386	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7903572	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7916848	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7919103	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs9420571	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9420572	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[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	esv2422237	chr10:91940542-92547558	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1052753	chr10:92081093-92565617	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv467432	chr10:92082250-92559908	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv551879	chr10:92082250-92559908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv467433	chr10:92083015-92598458	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv551880	chr10:92083015-92598458	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv516743	chr10:92083015-92605119	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1049931	chr10:92083932-92605364	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv948363	chr10:92084520-92614402	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv551882	chr10:92090785-92598823	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking 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	7 gene(s)	inside rSNPs	diseases
11	nsv1047255	chr10:92095431-92548184	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv540744	chr10:92095431-92548184	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1054504	chr10:92099335-92590723	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv533133	chr10:92363552-92594891	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1036058	chr10:92471568-92605364	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4933194	LIPK	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:92502800-92515800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr10:92503000-92515400	Weak transcription	HMEC	breast
3	chr10:92508800-92515400	Weak transcription	NHEK	skin
4	chr10:92509200-92514400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr10:92509200-92515400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr10:92509400-92516800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr10:92510600-92511400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr10:92510800-92511400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr10:92511000-92511600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:92511200-92511600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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