Variant report

Variant	rs4888374
Chromosome Location	chr16:75322228-75322229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr16:75322142-75322523	HUVEC	blood vessel:	n/a	n/a
2	MYC	chr16:75322217-75322261	MCF-7	breast:	n/a	n/a
3	TFAP2A	chr16:75321688-75322464	Hela-S3	cervix:	n/a	chr16:75322282-75322297
4	MAX	chr16:75321647-75322462	MCF-7	breast:	n/a	n/a
5	POLR2A	chr16:75321998-75322527	HUVEC	blood vessel:	n/a	n/a
6	NR2F2	chr16:75321682-75322535	MCF-7	breast:	n/a	n/a
7	TFAP2C	chr16:75321659-75322491	Hela-S3	cervix:	n/a	chr16:75322234-75322249 chr16:75322280-75322295 chr16:75321822-75321837
8	POLR2A	chr16:75322089-75323290	HL-60	blood:	n/a	n/a
9	POLR2A	chr16:75321644-75322840	PBDE	blood:	n/a	n/a
10	POLR2A	chr16:75322048-75323061	HL-60	blood:	n/a	n/a
11	SIN3AK20	chr16:75321539-75322726	MCF-7	breast:	n/a	n/a
12	MAX	chr16:75321772-75322892	NB4	blood:	n/a	n/a
13	MYC	chr16:75322161-75322875	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:75297370..75301171-chr16:75316900..75323378,8	MCF-7	breast:
2	chr16:75281206..75283355-chr16:75320437..75323255,2	MCF-7	breast:
3	chr16:75322113..75324158-chr16:75324406..75326106,2	MCF-7	breast:
4	chr16:75298337..75302151-chr16:75321880..75325464,5	MCF-7	breast:

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

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1011121	0.81[ASN][1000 genomes]
rs1017239	0.91[ASN][1000 genomes]
rs1074961	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10781976	0.80[ASN][1000 genomes]
rs10781977	0.92[ASN][1000 genomes]
rs10871307	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10871308	0.95[ASN][1000 genomes]
rs11149812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11149813	0.98[ASN][1000 genomes]
rs11149814	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11149816	0.90[ASN][1000 genomes]
rs11640018	0.80[ASN][1000 genomes]
rs11641532	0.81[ASN][1000 genomes]
rs11645691	0.86[ASN][1000 genomes]
rs11646418	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12445188	0.93[ASN][1000 genomes]
rs12445211	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12445813	0.94[ASN][1000 genomes]
rs12446903	0.88[ASN][1000 genomes]
rs12449177	0.98[ASN][1000 genomes]
rs12932952	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12935329	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12935787	0.80[ASN][1000 genomes]
rs1559339	0.81[ASN][1000 genomes]
rs17685540	0.81[ASN][1000 genomes]
rs1862705	0.94[ASN][1000 genomes]
rs1895489	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2032926	0.91[ASN][1000 genomes]
rs2059257	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2161648	0.81[ASN][1000 genomes]
rs247423	0.85[ASN][1000 genomes]
rs247424	0.84[ASN][1000 genomes]
rs247425	0.84[ASN][1000 genomes]
rs247427	0.88[ASN][1000 genomes]
rs247431	0.88[ASN][1000 genomes]
rs247434	0.87[ASN][1000 genomes]
rs247436	0.88[ASN][1000 genomes]
rs247437	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs247438	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2865527	0.85[ASN][1000 genomes]
rs2865532	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34029337	0.81[ASN][1000 genomes]
rs34624768	0.80[ASN][1000 genomes]
rs34673655	0.81[ASN][1000 genomes]
rs35937717	0.80[ASN][1000 genomes]
rs3743606	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3784936	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784937	0.95[ASN][1000 genomes]
rs3844219	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851735	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3851736	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4243111	0.81[ASN][1000 genomes]
rs4243112	0.81[ASN][1000 genomes]
rs4536500	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs455407	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs467223	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs467780	0.87[ASN][1000 genomes]
rs468079	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4887811	0.83[EUR][1000 genomes]
rs4887812	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4887813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4887814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887815	0.81[ASN][1000 genomes]
rs4887816	0.81[ASN][1000 genomes]
rs4888369	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4888370	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4888371	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4888372	0.81[ASN][1000 genomes]
rs4888375	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888376	0.81[ASN][1000 genomes]
rs4888378	0.80[ASN][1000 genomes]
rs4888381	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4888393	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888394	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888395	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888396	0.88[ASN][1000 genomes]
rs4888397	0.85[ASN][1000 genomes]
rs4888398	0.88[ASN][1000 genomes]
rs4993971	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6564245	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6564249	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6564256	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7187263	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7189407	0.87[ASN][1000 genomes]
rs7192155	0.88[ASN][1000 genomes]
rs7199680	0.85[ASN][1000 genomes]
rs7202284	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs766522	0.88[ASN][1000 genomes]
rs8046184	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8046949	0.88[ASN][1000 genomes]
rs8047811	0.85[ASN][1000 genomes]
rs8048677	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8048816	0.88[ASN][1000 genomes]
rs8049611	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8050662	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8051611	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8051785	0.88[ASN][1000 genomes]
rs8053632	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8054586	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8055609	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs889446	0.95[ASN][1000 genomes]
rs9933956	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9934007	0.88[ASN][1000 genomes]
rs9989421	0.88[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
rs4888374	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75301000-75325000	Weak transcription	Liver	Liver
2	chr16:75302000-75324000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr16:75306200-75325000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr16:75306200-75325200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr16:75307800-75323000	Weak transcription	NHLF	lung
6	chr16:75307800-75325400	Weak transcription	Osteobl	bone
7	chr16:75312000-75324400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr16:75313400-75324600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr16:75313400-75325200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr16:75313400-75325200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr16:75313600-75323200	Weak transcription	HepG2	liver
12	chr16:75313600-75323800	Weak transcription	Ovary	ovary
13	chr16:75313600-75325800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr16:75313600-75330400	Weak transcription	Pancreas	Pancrea
15	chr16:75314000-75325000	Weak transcription	Brain Anterior Caudate	brain
16	chr16:75314800-75325400	Weak transcription	Colon Smooth Muscle	Colon
17	chr16:75315000-75335600	Weak transcription	Psoas Muscle	Psoas
18	chr16:75315200-75325200	Weak transcription	Brain Hippocampus Middle	brain
19	chr16:75315200-75326600	Weak transcription	Brain Substantia Nigra	brain
20	chr16:75315400-75325400	Weak transcription	Aorta	Aorta
21	chr16:75316600-75323000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr16:75316800-75325000	Weak transcription	Brain Germinal Matrix	brain
23	chr16:75316800-75325200	Weak transcription	Primary B cells from cord blood	blood
24	chr16:75317000-75323800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr16:75317000-75325000	Weak transcription	Brain Angular Gyrus	brain
26	chr16:75317000-75325800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr16:75317000-75335600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr16:75317200-75322600	Weak transcription	Colonic Mucosa	Colon
29	chr16:75317200-75325000	Weak transcription	Fetal Brain Female	brain
30	chr16:75317200-75325200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr16:75317400-75358000	Weak transcription	Fetal Brain Male	brain
32	chr16:75318600-75323800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr16:75318600-75330200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr16:75318800-75325000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr16:75319000-75322600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr16:75319200-75324000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr16:75320200-75325200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr16:75320800-75323000	Genic enhancers	Fetal Muscle Leg	muscle
39	chr16:75320800-75339000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr16:75321000-75326800	Strong transcription	Fetal Intestine Small	intestine
41	chr16:75321200-75322400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr16:75321200-75322600	Enhancers	Spleen	Spleen
43	chr16:75321200-75323000	Enhancers	Placenta	Placenta
44	chr16:75321200-75323400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr16:75321200-75323400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
46	chr16:75321200-75326800	Strong transcription	Fetal Stomach	stomach
47	chr16:75321200-75329000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr16:75321400-75323000	Enhancers	GM12878-XiMat	blood
49	chr16:75321400-75323000	Enhancers	K562	blood
50	chr16:75321400-75323400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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