Variant report

Variant	rs247447
Chromosome Location	chr16:75486648-75486649
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	chr16:75486316..75489420-chr16:75490686..75493113,4	MCF-7	breast:
2	chr16:75482535..75486737-chr16:75496881..75499746,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166822	Chromatin interaction
ENSG00000261717	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1017239	0.82[JPT][hapmap]
rs1074961	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10781977	0.82[JPT][hapmap]
rs10871308	0.82[JPT][hapmap]
rs11149812	1.00[CEU][hapmap]
rs11646418	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12445813	0.81[JPT][hapmap]
rs12932952	0.83[EUR][1000 genomes]
rs1540	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs185052	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs185053	0.81[ASN][1000 genomes]
rs1862705	0.82[JPT][hapmap]
rs2059257	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2242405	0.90[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs247423	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs247424	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs247425	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs247427	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs247431	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs247434	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs247436	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs247437	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs247438	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs247443	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247450	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs37588	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs37589	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs37596	0.85[ASN][1000 genomes]
rs37599	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37601	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs37602	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37605	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3784936	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs3844219	0.83[EUR][1000 genomes]
rs3851735	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs3851736	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs40217	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs42472	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4536500	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap]
rs455407	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs467223	0.88[AMR][1000 genomes]
rs467780	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs468079	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4887827	0.82[ASN][1000 genomes]
rs4887828	0.89[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs4888393	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4888394	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4888395	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4888396	0.82[JPT][hapmap]
rs4993971	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62062595	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6564256	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7187690	0.93[CEU][hapmap]
rs7189407	0.80[JPT][hapmap]
rs7201989	0.93[ASN][1000 genomes]
rs7202284	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs766522	0.82[JPT][hapmap]
rs8046184	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8046416	0.83[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs8048677	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8048816	0.82[JPT][hapmap]
rs8049611	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8050662	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.94[TSI][hapmap]
rs8051611	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8053632	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs8054586	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8055609	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs977986	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9923834	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9928232	0.84[ASN][1000 genomes]
rs9934007	0.82[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	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	nsv521596	chr16:75466696-75486648	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs247447	TMEM170A	cis	parietal	SCAN
rs247447	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75468400-75489400	Weak transcription	Small Intestine	intestine
2	chr16:75468600-75487800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:75468600-75489800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr16:75468800-75489200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr16:75468800-75493800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr16:75468800-75497000	Weak transcription	NHLF	lung
7	chr16:75469400-75491000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr16:75469400-75497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:75469400-75497400	Weak transcription	Psoas Muscle	Psoas
10	chr16:75473600-75496000	Weak transcription	HMEC	breast
11	chr16:75477000-75487000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr16:75477400-75494400	Weak transcription	NH-A	brain
13	chr16:75477800-75497000	Weak transcription	NHDF-Ad	bronchial
14	chr16:75478600-75486800	Weak transcription	Ovary	ovary
15	chr16:75479200-75487200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr16:75479400-75493800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr16:75479600-75486800	Weak transcription	Colon Smooth Muscle	Colon
18	chr16:75481000-75489600	Weak transcription	Colonic Mucosa	Colon
19	chr16:75481800-75497600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr16:75482400-75494200	Weak transcription	GM12878-XiMat	blood
21	chr16:75483200-75495800	Weak transcription	Fetal Brain Male	brain
22	chr16:75483600-75494200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:75483800-75496000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr16:75484000-75487800	Weak transcription	Osteobl	bone
25	chr16:75484000-75490800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr16:75484000-75496600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr16:75484000-75496800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr16:75484600-75489800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr16:75485000-75489400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr16:75485000-75494400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr16:75485200-75489400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr16:75485200-75490000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr16:75485200-75493200	Weak transcription	Esophagus	oesophagus
34	chr16:75485400-75487800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr16:75485400-75493200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr16:75485400-75496800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr16:75485600-75487800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr16:75485600-75487800	Weak transcription	Adipose Nuclei	Adipose
39	chr16:75485600-75487800	Weak transcription	Spleen	Spleen
40	chr16:75485600-75488600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr16:75485600-75489800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr16:75485600-75491000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr16:75485600-75491000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr16:75485600-75491200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr16:75485600-75493800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr16:75485600-75494200	Weak transcription	Brain Germinal Matrix	brain
47	chr16:75485600-75495800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr16:75485600-75496400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr16:75485600-75497200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr16:75485800-75486800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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