Variant report

Variant	rs42472
Chromosome Location	chr16:75473320-75473321
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75465554..75469979-chr16:75471848..75474858,4	MCF-7	breast:
2	chr16:75466767..75471192-chr16:75472860..75476698,4	K562	blood:
3	chr16:75466281..75469140-chr16:75472211..75473789,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1017239	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1074961	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10781977	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10871308	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs11149812	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[YRI][hapmap]
rs11149813	0.94[CHB][hapmap]
rs11149832	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11645691	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs11646418	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12445813	0.80[JPT][hapmap]
rs12446903	0.81[ASN][1000 genomes]
rs12917651	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12929673	0.81[ASN][1000 genomes]
rs12932952	0.85[EUR][1000 genomes]
rs1540	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1542864	0.81[ASN][1000 genomes]
rs185052	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1862705	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2059257	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2242405	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs247423	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247424	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs247425	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs247427	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247431	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247434	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs247436	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247437	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs247438	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247442	0.80[EUR][1000 genomes]
rs247443	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247447	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]
rs247450	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2865527	0.81[ASN][1000 genomes]
rs35209155	0.81[ASN][1000 genomes]
rs37588	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37589	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37599	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs37601	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs37602	1.00[CEU][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs37605	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3784936	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3844219	0.85[EUR][1000 genomes]
rs3851735	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs3851736	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs40217	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4536500	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs455407	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs467223	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs467780	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs468079	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4887825	0.81[ASN][1000 genomes]
rs4887828	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs4888381	0.82[EUR][1000 genomes]
rs4888393	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4888394	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4888395	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4888396	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4888398	0.81[ASN][1000 genomes]
rs4993971	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62062595	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6564249	0.82[EUR][1000 genomes]
rs6564256	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7187690	0.93[CEU][hapmap]
rs7189407	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs7201989	0.99[ASN][1000 genomes]
rs7202284	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes]
rs766522	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs8046184	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8046416	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs8046949	0.81[ASN][1000 genomes]
rs8048677	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8048816	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs8049611	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8050662	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs8051611	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8053632	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs8054586	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8055609	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8055974	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs977986	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9923834	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9934007	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs9989421	0.81[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	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	nsv516019	chr16:75466696-75473332	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs42472	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75468400-75482400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:75468400-75482600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:75468400-75489400	Weak transcription	Small Intestine	intestine
4	chr16:75468600-75476800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:75468600-75481000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr16:75468600-75481600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr16:75468600-75482400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:75468600-75487800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr16:75468600-75489800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr16:75468800-75476000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr16:75468800-75478800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr16:75468800-75479000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr16:75468800-75479200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:75468800-75479200	Weak transcription	Left Ventricle	heart
15	chr16:75468800-75479400	Weak transcription	Fetal Intestine Large	intestine
16	chr16:75468800-75480400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr16:75468800-75480400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr16:75468800-75480600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:75468800-75480600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr16:75468800-75480600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr16:75468800-75480600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr16:75468800-75480800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr16:75468800-75481000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr16:75468800-75481000	Weak transcription	Primary T cells from cord blood	blood
25	chr16:75468800-75481000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:75468800-75481000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr16:75468800-75481000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr16:75468800-75481000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr16:75468800-75481000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr16:75468800-75481000	Weak transcription	HSMM	muscle
31	chr16:75468800-75481400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr16:75468800-75483000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr16:75468800-75483200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr16:75468800-75483600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr16:75468800-75483600	Weak transcription	Adipose Nuclei	Adipose
36	chr16:75468800-75483600	Weak transcription	Hela-S3	cervix
37	chr16:75468800-75483800	Weak transcription	HSMMtube	muscle
38	chr16:75468800-75484200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr16:75468800-75484400	Weak transcription	Brain Anterior Caudate	brain
40	chr16:75468800-75484400	Weak transcription	NHEK	skin
41	chr16:75468800-75484600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr16:75468800-75484600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr16:75468800-75484600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr16:75468800-75484800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr16:75468800-75484800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr16:75468800-75485400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr16:75468800-75486400	Weak transcription	Pancreas	Pancrea
48	chr16:75468800-75486400	Weak transcription	Right Atrium	heart
49	chr16:75468800-75486600	Weak transcription	HUVEC	blood vessel
50	chr16:75468800-75489200	Weak transcription	Brain Cingulate Gyrus	brain

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