Variant report

Variant	rs247431
Chromosome Location	chr16:75440861-75440862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:75440851..75444308-chr16:75465493..75468084,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 204 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:196)

rs_ID	r²[population]
rs1017239	0.94[ASN][1000 genomes]
rs10431974	0.82[ASN][1000 genomes]
rs10514396	0.82[ASN][1000 genomes]
rs1074961	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10781977	0.88[ASN][1000 genomes]
rs10871307	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10871308	0.91[ASN][1000 genomes]
rs10871311	0.81[ASN][1000 genomes]
rs1109341	0.82[ASN][1000 genomes]
rs1109342	0.82[ASN][1000 genomes]
rs11149812	0.88[ASN][1000 genomes]
rs11149813	0.88[ASN][1000 genomes]
rs11149814	0.88[ASN][1000 genomes]
rs11149816	0.91[ASN][1000 genomes]
rs11149818	0.82[ASN][1000 genomes]
rs11149820	0.82[ASN][1000 genomes]
rs11149822	0.81[ASN][1000 genomes]
rs11149824	0.82[ASN][1000 genomes]
rs11149825	0.82[ASN][1000 genomes]
rs11149828	0.81[ASN][1000 genomes]
rs11149829	0.82[ASN][1000 genomes]
rs11149831	0.81[ASN][1000 genomes]
rs11640674	0.81[ASN][1000 genomes]
rs11643410	0.82[ASN][1000 genomes]
rs11644592	0.81[ASN][1000 genomes]
rs11645691	0.99[ASN][1000 genomes]
rs11646418	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11646677	0.81[ASN][1000 genomes]
rs11858992	0.81[ASN][1000 genomes]
rs11860284	0.81[ASN][1000 genomes]
rs11862582	0.81[ASN][1000 genomes]
rs11864102	0.81[ASN][1000 genomes]
rs11865004	0.81[ASN][1000 genomes]
rs12051136	0.82[ASN][1000 genomes]
rs12051326	0.82[ASN][1000 genomes]
rs12149063	0.81[ASN][1000 genomes]
rs12443834	0.82[ASN][1000 genomes]
rs12443904	0.82[ASN][1000 genomes]
rs12445188	0.90[ASN][1000 genomes]
rs12445211	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12445813	0.91[ASN][1000 genomes]
rs12446903	1.00[ASN][1000 genomes]
rs12449177	0.88[ASN][1000 genomes]
rs12599361	0.82[ASN][1000 genomes]
rs12922897	0.90[ASN][1000 genomes]
rs12924782	0.81[ASN][1000 genomes]
rs12924920	0.81[ASN][1000 genomes]
rs12932952	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12935329	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1364079	0.81[ASN][1000 genomes]
rs1540	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1544810	0.81[ASN][1000 genomes]
rs1549306	0.80[ASN][1000 genomes]
rs17696696	0.81[ASN][1000 genomes]
rs1808434	0.81[ASN][1000 genomes]
rs1808435	0.81[ASN][1000 genomes]
rs1808436	0.81[ASN][1000 genomes]
rs185052	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1862705	0.92[ASN][1000 genomes]
rs1895489	0.86[ASN][1000 genomes]
rs1895490	0.81[ASN][1000 genomes]
rs2032926	0.94[ASN][1000 genomes]
rs2059256	0.81[ASN][1000 genomes]
rs2059257	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2113232	0.80[ASN][1000 genomes]
rs2242405	0.84[ASN][1000 genomes]
rs2285222	0.81[ASN][1000 genomes]
rs2285224	0.81[ASN][1000 genomes]
rs2285225	0.81[ASN][1000 genomes]
rs247423	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247424	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247425	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs247427	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247434	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247436	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247437	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247438	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247439	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs247443	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs247447	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs247450	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2865527	0.96[ASN][1000 genomes]
rs2865530	0.80[ASN][1000 genomes]
rs2865531	0.80[ASN][1000 genomes]
rs2865532	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2903033	0.80[ASN][1000 genomes]
rs34296964	0.81[ASN][1000 genomes]
rs35263058	0.81[ASN][1000 genomes]
rs35552529	0.81[ASN][1000 genomes]
rs35737321	0.82[ASN][1000 genomes]
rs3743606	0.86[ASN][1000 genomes]
rs37588	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs37589	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs37599	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs37601	0.84[AMR][1000 genomes]
rs37602	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs37605	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3784936	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3784937	0.91[ASN][1000 genomes]
rs3844219	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851735	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851736	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851739	0.86[ASN][1000 genomes]
rs3863446	0.81[ASN][1000 genomes]
rs40217	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4146809	0.80[ASN][1000 genomes]
rs4146810	0.80[ASN][1000 genomes]
rs42472	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4536500	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs455407	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638613	0.82[ASN][1000 genomes]
rs467223	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs467780	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs468079	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887813	0.86[ASN][1000 genomes]
rs4887814	0.88[ASN][1000 genomes]
rs4887823	0.82[ASN][1000 genomes]
rs4887824	0.82[ASN][1000 genomes]
rs4887828	0.83[ASN][1000 genomes]
rs4888374	0.88[ASN][1000 genomes]
rs4888375	0.88[ASN][1000 genomes]
rs4888381	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4888385	0.80[ASN][1000 genomes]
rs4888386	0.80[ASN][1000 genomes]
rs4888387	0.80[ASN][1000 genomes]
rs4888388	0.81[ASN][1000 genomes]
rs4888389	0.81[ASN][1000 genomes]
rs4888393	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4888394	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4888395	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4888396	1.00[ASN][1000 genomes]
rs4888397	0.97[ASN][1000 genomes]
rs4888398	1.00[ASN][1000 genomes]
rs4888403	0.82[ASN][1000 genomes]
rs4888404	0.82[ASN][1000 genomes]
rs4888405	0.82[ASN][1000 genomes]
rs4888406	0.82[ASN][1000 genomes]
rs4888407	0.82[ASN][1000 genomes]
rs4888409	0.82[ASN][1000 genomes]
rs4888410	0.82[ASN][1000 genomes]
rs4888414	0.81[ASN][1000 genomes]
rs4888415	0.81[ASN][1000 genomes]
rs4993969	0.81[ASN][1000 genomes]
rs4993970	0.81[ASN][1000 genomes]
rs4993971	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56343285	0.81[ASN][1000 genomes]
rs60730309	0.82[ASN][1000 genomes]
rs62062564	0.81[ASN][1000 genomes]
rs62062565	0.81[ASN][1000 genomes]
rs62062567	0.81[ASN][1000 genomes]
rs62062568	0.81[ASN][1000 genomes]
rs62062595	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6564249	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6564256	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6564258	0.81[ASN][1000 genomes]
rs7184525	0.82[ASN][1000 genomes]
rs7185640	0.81[ASN][1000 genomes]
rs7188231	0.82[ASN][1000 genomes]
rs7188604	0.81[ASN][1000 genomes]
rs7189407	0.84[ASN][1000 genomes]
rs7192155	0.93[ASN][1000 genomes]
rs7199132	0.81[ASN][1000 genomes]
rs7199680	0.89[ASN][1000 genomes]
rs7201989	0.82[ASN][1000 genomes]
rs7202284	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7203157	0.82[ASN][1000 genomes]
rs7206541	0.81[ASN][1000 genomes]
rs72787160	0.82[ASN][1000 genomes]
rs7499872	0.82[ASN][1000 genomes]
rs766521	0.82[ASN][1000 genomes]
rs766522	1.00[ASN][1000 genomes]
rs8046000	0.81[ASN][1000 genomes]
rs8046184	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8046416	0.82[ASN][1000 genomes]
rs8046949	1.00[ASN][1000 genomes]
rs8048527	0.82[ASN][1000 genomes]
rs8048677	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8048816	1.00[ASN][1000 genomes]
rs8049611	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8050662	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8051407	0.82[ASN][1000 genomes]
rs8051611	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8051785	0.91[ASN][1000 genomes]
rs8053632	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8054586	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8055609	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8056080	0.81[ASN][1000 genomes]
rs8056236	0.82[ASN][1000 genomes]
rs8057203	0.81[ASN][1000 genomes]
rs8057849	0.82[ASN][1000 genomes]
rs889446	0.91[ASN][1000 genomes]
rs977986	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9923834	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9933956	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9934007	0.98[ASN][1000 genomes]
rs9989421	1.00[ASN][1000 genomes]

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	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	esv2422358	chr16:75381762-75456763	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv1062023	chr16:75427013-75461626	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs247431	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75406000-75453400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:75407200-75454200	Weak transcription	Stomach Mucosa	stomach
3	chr16:75409200-75445400	Weak transcription	Colonic Mucosa	Colon
4	chr16:75412600-75446000	Weak transcription	Brain Substantia Nigra	brain
5	chr16:75415400-75443200	Weak transcription	Small Intestine	intestine
6	chr16:75415600-75453400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr16:75425400-75454200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr16:75425400-75457200	Weak transcription	Fetal Brain Male	brain
9	chr16:75427000-75443400	Weak transcription	Hela-S3	cervix
10	chr16:75427200-75441600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr16:75427200-75443400	Weak transcription	Fetal Kidney	kidney
12	chr16:75427200-75445000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr16:75427200-75445400	Weak transcription	Brain Angular Gyrus	brain
14	chr16:75427200-75445400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr16:75427200-75445400	Weak transcription	A549	lung
16	chr16:75427200-75445400	Weak transcription	K562	blood
17	chr16:75427200-75446200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr16:75427200-75449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr16:75427200-75464400	Weak transcription	Esophagus	oesophagus
20	chr16:75427200-75465400	Weak transcription	Spleen	Spleen
21	chr16:75427600-75441000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr16:75428200-75453400	Weak transcription	Psoas Muscle	Psoas
23	chr16:75428400-75441600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr16:75429000-75443200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr16:75429000-75445000	Weak transcription	Lung	lung
26	chr16:75429000-75454400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr16:75429000-75454800	Weak transcription	HMEC	breast
28	chr16:75429200-75441000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr16:75429200-75441400	Weak transcription	Colon Smooth Muscle	Colon
30	chr16:75429200-75441600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr16:75429200-75441800	Weak transcription	Brain Germinal Matrix	brain
32	chr16:75429200-75441800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr16:75429200-75443000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr16:75429200-75443000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr16:75429200-75443200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr16:75429200-75445000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr16:75429200-75453400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr16:75429200-75454800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr16:75429200-75455000	Weak transcription	Gastric	stomach
40	chr16:75429400-75441000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr16:75429400-75441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr16:75432400-75445200	Weak transcription	Brain Hippocampus Middle	brain
43	chr16:75432400-75465400	Weak transcription	Pancreas	Pancrea
44	chr16:75432400-75466600	Weak transcription	Aorta	Aorta
45	chr16:75432600-75441600	Weak transcription	Left Ventricle	heart
46	chr16:75432600-75443000	Weak transcription	Liver	Liver
47	chr16:75432600-75443600	Weak transcription	Primary B cells from cord blood	blood
48	chr16:75432600-75445000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr16:75432600-75446000	Weak transcription	Right Ventricle	heart
50	chr16:75432600-75446400	Weak transcription	Right Atrium	heart

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