Variant report

Variant	rs10871313
Chromosome Location	chr16:75507094-75507095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:75505900..75508078-chr16:75510609..75513420,3	MCF-7	breast:
2	chr16:75505198..75507754-chr16:75508642..75511329,3	MCF-7	breast:
3	chr16:75505256..75507400-chr16:75525903..75527940,2	MCF-7	breast:
4	chr16:75506694..75509130-chr16:75514124..75517050,2	MCF-7	breast:
5	chr16:75497168..75499078-chr16:75505680..75507932,2	MCF-7	breast:
6	chr16:75506243..75508903-chr16:75511656..75514124,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHST6-2	chr16:75507025-75507817	NONHSAT143740

No data

Variant related genes	Relation type
ENSG00000166822	Chromatin interaction
ENSG00000203472	Chromatin interaction
ENSG00000261717	Chromatin interaction

Extended variants
information (count: 154 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs100912	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1011121	0.86[CHB][hapmap]
rs1030261	0.95[ASN][1000 genomes]
rs1030262	0.97[ASN][1000 genomes]
rs10514393	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs10514396	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs10781976	0.86[CHB][hapmap]
rs10871312	0.95[ASN][1000 genomes]
rs1109342	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs11149815	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs11149831	0.86[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs11640018	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11641249	0.97[ASN][1000 genomes]
rs11641430	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11641532	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs11643207	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11644306	0.96[ASN][1000 genomes]
rs11646677	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs11649638	0.95[ASN][1000 genomes]
rs11865296	0.81[ASN][1000 genomes]
rs12051137	0.97[ASN][1000 genomes]
rs12149063	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12444589	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12446877	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12448829	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12918797	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12924333	0.93[ASN][1000 genomes]
rs12927562	0.94[ASN][1000 genomes]
rs12928036	0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs12932606	0.83[ASN][1000 genomes]
rs12933281	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1364078	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs1424013	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549306	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs1559339	0.86[CHB][hapmap]
rs166013	0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs17696696	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs17696749	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs17696831	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1834013	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1834014	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1862706	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs1895490	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2059256	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs2161648	0.86[CHB][hapmap]
rs2161684	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs247454	0.89[ASN][1000 genomes]
rs2738809	0.90[ASN][1000 genomes]
rs2738812	0.83[ASN][1000 genomes]
rs2738813	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2738814	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28558946	0.95[ASN][1000 genomes]
rs2865530	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2865531	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs28655617	0.94[ASN][1000 genomes]
rs2903033	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs3115960	0.83[CEU][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34021527	0.84[ASN][1000 genomes]
rs34539062	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34918083	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34996006	0.92[ASN][1000 genomes]
rs35214308	0.92[ASN][1000 genomes]
rs35263058	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs35683383	0.93[ASN][1000 genomes]
rs3743607	0.84[JPT][hapmap]
rs37592	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37593	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37594	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37595	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37597	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs37599	0.81[ASN][1000 genomes]
rs37602	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs37605	0.82[ASN][1000 genomes]
rs37606	0.97[ASN][1000 genomes]
rs3851733	0.89[JPT][hapmap]
rs3863445	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs40446	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4146809	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4146810	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4243111	0.86[CHB][hapmap]
rs4638613	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4887823	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4887824	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4887828	0.85[CHB][hapmap]
rs4887829	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4888376	0.86[CHB][hapmap]
rs4888377	0.89[CHB][hapmap]
rs4888378	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4888379	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4888380	0.89[JPT][hapmap]
rs4888383	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4888386	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4888387	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs4888388	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4888389	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4888393	0.81[CHB][hapmap]
rs4888405	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4888415	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs4888416	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4888425	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4888426	0.92[ASN][1000 genomes]
rs4888427	0.93[ASN][1000 genomes]
rs4888430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4888431	0.96[ASN][1000 genomes]
rs4888432	0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs4993969	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs56004344	0.85[ASN][1000 genomes]
rs56116092	0.95[ASN][1000 genomes]
rs59155720	0.93[ASN][1000 genomes]
rs59347518	0.90[ASN][1000 genomes]
rs59465235	0.94[ASN][1000 genomes]
rs62060550	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62060551	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6564261	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7188604	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7191890	0.81[ASN][1000 genomes]
rs7193828	0.91[ASN][1000 genomes]
rs7194035	0.91[ASN][1000 genomes]
rs7195161	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7198873	0.90[ASN][1000 genomes]
rs7199062	0.92[ASN][1000 genomes]
rs7199132	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs7200053	0.92[ASN][1000 genomes]
rs7202596	0.96[ASN][1000 genomes]
rs7203157	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7204984	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7206665	0.92[ASN][1000 genomes]
rs766521	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs8046109	0.89[JPT][hapmap]
rs8046416	0.82[CHB][hapmap]
rs8050059	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs8055490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8055974	0.82[CHB][hapmap]
rs8056141	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8057084	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8063068	0.97[ASN][1000 genomes]
rs977985	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977986	0.82[ASN][1000 genomes]
rs977987	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9922008	0.84[CHB][hapmap]
rs9923834	0.82[ASN][1000 genomes]
rs9933255	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	esv2758432	chr16:75419614-75576971	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	esv2758657	chr16:75419614-75576971	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv457521	chr16:75487758-75603925	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv572979	chr16:75487758-75603925	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
10	esv3485939	chr16:75497453-75550284	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	esv3485940	chr16:75497453-75550284	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv572980	chr16:75505046-75549885	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10871313	RP11-252K23.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10871313	CFDP1	Cis_1M	lymphoblastoid	RTeQTL
rs10871313	RP11-252K23.2	cis	Thyroid	GTEx
rs10871313	RP11-252K23.2	cis	Nerve Tibial	GTEx
rs10871313	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs10871313	RP11-252K23.2	cis	Artery Tibial	GTEx
rs10871313	RP11-252K23.2	cis	lung	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75498600-75511800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:75498800-75507200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:75498800-75518600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr16:75499000-75511000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr16:75499000-75511200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr16:75499000-75511200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr16:75499200-75511400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr16:75499200-75511400	Weak transcription	Brain Anterior Caudate	brain
9	chr16:75499200-75519600	Weak transcription	Fetal Intestine Small	intestine
10	chr16:75502400-75518200	Weak transcription	Aorta	Aorta
11	chr16:75505400-75507200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr16:75505400-75512600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr16:75506000-75512600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr16:75506200-75509000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr16:75506200-75511600	Weak transcription	Brain Hippocampus Middle	brain
16	chr16:75506200-75517000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr16:75506400-75510800	Weak transcription	Hela-S3	cervix
18	chr16:75506600-75511000	Weak transcription	HMEC	breast
19	chr16:75506800-75507200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr16:75506800-75507200	Strong transcription	Brain Substantia Nigra	brain
21	chr16:75506800-75510800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr16:75506800-75511400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr16:75506800-75512200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr16:75506800-75512400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr16:75506800-75514200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr16:75506800-75520400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr16:75507000-75507200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
28	chr16:75507000-75509400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr16:75507000-75512400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr16:75507000-75517600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr16:75507000-75525600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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