Variant report

Variant	rs247436
Chromosome Location	chr16:75445971-75445972
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	chr16:75445412..75447082-chr16:75465905..75468700,2	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	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10781977	0.88[ASN][1000 genomes]
rs10871307	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	0.85[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	0.82[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	0.88[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	0.92[AMR][1000 genomes];0.94[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	0.98[AMR][1000 genomes];0.93[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	0.84[AMR][1000 genomes];0.90[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	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247424	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247425	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs247427	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247431	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247434	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247437	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247438	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247439	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs247443	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs247447	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs247450	0.92[AMR][1000 genomes];0.93[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	0.82[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	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs37589	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs37599	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37601	0.82[AMR][1000 genomes]
rs37602	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs37605	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3784936	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3784937	0.91[ASN][1000 genomes]
rs3844219	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851735	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851736	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851739	0.86[ASN][1000 genomes]
rs3863446	0.81[ASN][1000 genomes]
rs40217	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4146809	0.80[ASN][1000 genomes]
rs4146810	0.80[ASN][1000 genomes]
rs42472	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4536500	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs455407	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638613	0.82[ASN][1000 genomes]
rs467223	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs467780	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs468079	0.94[AMR][1000 genomes];0.92[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	0.84[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	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4888394	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4888395	0.96[AMR][1000 genomes];0.92[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	0.94[AMR][1000 genomes];0.92[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	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6564249	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6564256	0.84[AMR][1000 genomes];0.90[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	0.89[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	0.94[AMR][1000 genomes];0.92[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	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8048816	1.00[ASN][1000 genomes]
rs8049611	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8050662	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8051407	0.82[ASN][1000 genomes]
rs8051611	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8051785	0.91[ASN][1000 genomes]
rs8053632	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8054586	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8055609	0.84[AMR][1000 genomes];0.92[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	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9923834	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9933956	0.81[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
rs247436	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	chr16:75412600-75446000	Weak transcription	Brain Substantia Nigra	brain
4	chr16:75415600-75453400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr16:75425400-75454200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr16:75425400-75457200	Weak transcription	Fetal Brain Male	brain
7	chr16:75427200-75446200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr16:75427200-75449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:75427200-75464400	Weak transcription	Esophagus	oesophagus
10	chr16:75427200-75465400	Weak transcription	Spleen	Spleen
11	chr16:75428200-75453400	Weak transcription	Psoas Muscle	Psoas
12	chr16:75429000-75454400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr16:75429000-75454800	Weak transcription	HMEC	breast
14	chr16:75429200-75453400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr16:75429200-75454800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr16:75429200-75455000	Weak transcription	Gastric	stomach
17	chr16:75432400-75465400	Weak transcription	Pancreas	Pancrea
18	chr16:75432400-75466600	Weak transcription	Aorta	Aorta
19	chr16:75432600-75446000	Weak transcription	Right Ventricle	heart
20	chr16:75432600-75446400	Weak transcription	Right Atrium	heart
21	chr16:75436800-75446200	Weak transcription	NHLF	lung
22	chr16:75437000-75447600	Strong transcription	Fetal Intestine Small	intestine
23	chr16:75437200-75448400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr16:75437200-75454200	Weak transcription	Fetal Heart	heart
25	chr16:75438200-75446600	Strong transcription	Fetal Intestine Large	intestine
26	chr16:75438400-75446800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr16:75438400-75446800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr16:75438400-75448200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:75438400-75448600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr16:75438400-75448800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr16:75438600-75446800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr16:75438600-75447200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:75438600-75448600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr16:75438600-75448600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr16:75438800-75446800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr16:75438800-75447200	Strong transcription	Fetal Thymus	thymus
37	chr16:75439000-75448600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr16:75439200-75447400	Strong transcription	Fetal Muscle Leg	muscle
39	chr16:75439200-75447400	Strong transcription	Fetal Stomach	stomach
40	chr16:75439400-75446800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr16:75439600-75447400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr16:75439600-75447400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr16:75439800-75446400	Strong transcription	Adipose Nuclei	Adipose
44	chr16:75439800-75447800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr16:75440000-75446800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr16:75440000-75447000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr16:75440000-75447200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr16:75440200-75446200	Weak transcription	Fetal Lung	lung
49	chr16:75440400-75447400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr16:75440600-75448600	Strong transcription	Primary T cells from cord blood	blood

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