Variant report

Variant	rs1895489
Chromosome Location	chr16:75324781-75324782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75324277-75325142	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75323194..75324994-chr16:75337931..75340370,2	MCF-7	breast:
2	chr16:75311909..75314850-chr16:75324692..75326248,2	MCF-7	breast:
3	chr16:75283878..75286370-chr16:75323655..75326662,3	MCF-7	breast:
4	chr16:75298337..75302151-chr16:75321880..75325464,5	MCF-7	breast:
5	chr16:75322113..75324158-chr16:75324406..75326106,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-758P	TF binding region
ENSG00000153774	Chromatin interaction
ENSG00000050820	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1017239	0.90[ASN][1000 genomes]
rs1074961	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10781977	0.94[ASN][1000 genomes]
rs10871307	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10871308	0.94[ASN][1000 genomes]
rs11149812	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11149813	0.96[ASN][1000 genomes]
rs11149814	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11149816	0.88[ASN][1000 genomes]
rs11645691	0.85[ASN][1000 genomes]
rs11646418	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12445188	0.92[ASN][1000 genomes]
rs12445211	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12445813	0.92[ASN][1000 genomes]
rs12446903	0.86[ASN][1000 genomes]
rs12449177	0.96[ASN][1000 genomes]
rs12932952	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12935329	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862705	0.93[ASN][1000 genomes]
rs2032926	0.90[ASN][1000 genomes]
rs2059257	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs247423	0.82[ASN][1000 genomes]
rs247424	0.81[ASN][1000 genomes]
rs247425	0.82[ASN][1000 genomes]
rs247427	0.86[ASN][1000 genomes]
rs247431	0.86[ASN][1000 genomes]
rs247434	0.86[ASN][1000 genomes]
rs247436	0.86[ASN][1000 genomes]
rs247437	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs247438	0.86[ASN][1000 genomes]
rs2865527	0.82[ASN][1000 genomes]
rs2865532	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3743606	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3784936	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784937	0.94[ASN][1000 genomes]
rs3844219	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851735	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851736	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4536500	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs455407	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs467223	0.86[ASN][1000 genomes]
rs467780	0.86[ASN][1000 genomes]
rs468079	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4887812	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887813	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4887814	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4888369	0.84[EUR][1000 genomes]
rs4888370	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888371	0.87[ASN][1000 genomes]
rs4888374	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4888375	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4888381	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4888393	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4888394	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4888395	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4888396	0.86[ASN][1000 genomes]
rs4888397	0.84[ASN][1000 genomes]
rs4888398	0.86[ASN][1000 genomes]
rs4993971	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6564245	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6564249	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6564256	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7187263	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7189407	0.86[ASN][1000 genomes]
rs7192155	0.86[ASN][1000 genomes]
rs7199680	0.84[ASN][1000 genomes]
rs7202284	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs766522	0.86[ASN][1000 genomes]
rs8046184	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8046949	0.86[ASN][1000 genomes]
rs8047811	0.86[ASN][1000 genomes]
rs8048677	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8048816	0.86[ASN][1000 genomes]
rs8049611	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8050662	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8051611	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8051785	0.87[ASN][1000 genomes]
rs8053632	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8054586	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8055609	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs889446	0.94[ASN][1000 genomes]
rs9933956	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9934007	0.87[ASN][1000 genomes]
rs9989421	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	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
4	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	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
7	nsv833283	chr16:75302175-75392308	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1895489	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75301000-75325000	Weak transcription	Liver	Liver
2	chr16:75306200-75325000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr16:75306200-75325200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr16:75307800-75325400	Weak transcription	Osteobl	bone
5	chr16:75313400-75325200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr16:75313400-75325200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr16:75313600-75325800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr16:75313600-75330400	Weak transcription	Pancreas	Pancrea
9	chr16:75314000-75325000	Weak transcription	Brain Anterior Caudate	brain
10	chr16:75314800-75325400	Weak transcription	Colon Smooth Muscle	Colon
11	chr16:75315000-75335600	Weak transcription	Psoas Muscle	Psoas
12	chr16:75315200-75325200	Weak transcription	Brain Hippocampus Middle	brain
13	chr16:75315200-75326600	Weak transcription	Brain Substantia Nigra	brain
14	chr16:75315400-75325400	Weak transcription	Aorta	Aorta
15	chr16:75316800-75325000	Weak transcription	Brain Germinal Matrix	brain
16	chr16:75316800-75325200	Weak transcription	Primary B cells from cord blood	blood
17	chr16:75317000-75325000	Weak transcription	Brain Angular Gyrus	brain
18	chr16:75317000-75325800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr16:75317000-75335600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr16:75317200-75325000	Weak transcription	Fetal Brain Female	brain
21	chr16:75317200-75325200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr16:75317400-75358000	Weak transcription	Fetal Brain Male	brain
23	chr16:75318600-75330200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr16:75318800-75325000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr16:75320200-75325200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr16:75320800-75339000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:75321000-75326800	Strong transcription	Fetal Intestine Small	intestine
28	chr16:75321200-75326800	Strong transcription	Fetal Stomach	stomach
29	chr16:75321200-75329000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr16:75321600-75330600	Strong transcription	Fetal Lung	lung
31	chr16:75321800-75337600	Weak transcription	A549	lung
32	chr16:75322000-75325400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr16:75322000-75332200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr16:75322000-75337600	Strong transcription	Fetal Intestine Large	intestine
35	chr16:75322200-75325800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr16:75322200-75325800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr16:75322200-75326800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr16:75322200-75328600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr16:75322400-75325600	Weak transcription	Gastric	stomach
40	chr16:75322400-75338000	Weak transcription	Stomach Mucosa	stomach
41	chr16:75322600-75326000	Weak transcription	Fetal Kidney	kidney
42	chr16:75322600-75327200	Weak transcription	HSMM	muscle
43	chr16:75322800-75325000	Weak transcription	HSMMtube	muscle
44	chr16:75322800-75325200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr16:75322800-75329000	Weak transcription	Right Atrium	heart
46	chr16:75322800-75332200	Weak transcription	Small Intestine	intestine
47	chr16:75322800-75335600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr16:75323000-75325000	Weak transcription	Placenta	Placenta
49	chr16:75323000-75325200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr16:75323000-75328000	Strong transcription	Fetal Muscle Trunk	muscle

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