Variant report

Variant	rs1017239
Chromosome Location	chr16:75358207-75358208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 143 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10514393	0.87[JPT][hapmap]
rs10514396	0.83[JPT][hapmap]
rs1074961	0.96[ASN][1000 genomes]
rs10781977	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10871307	0.93[ASN][1000 genomes]
rs10871308	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1109342	0.83[JPT][hapmap]
rs11149812	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11149813	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11149814	0.92[ASN][1000 genomes]
rs11149815	0.88[JPT][hapmap]
rs11149816	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11149831	0.83[JPT][hapmap]
rs11645691	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11646418	0.99[ASN][1000 genomes]
rs12149063	0.83[JPT][hapmap]
rs12445188	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12445211	0.97[ASN][1000 genomes]
rs12445813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12446903	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12449177	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12922897	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12922951	0.80[ASN][1000 genomes]
rs12932952	0.94[ASN][1000 genomes]
rs12935329	0.94[ASN][1000 genomes]
rs1364078	0.84[JPT][hapmap]
rs1540	0.80[ASN][1000 genomes]
rs1549306	0.83[JPT][hapmap]
rs17696696	0.83[JPT][hapmap]
rs185052	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1862705	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1862706	0.82[JPT][hapmap]
rs1895489	0.90[ASN][1000 genomes]
rs1895490	0.83[JPT][hapmap]
rs2032926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059256	0.83[JPT][hapmap]
rs2059257	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2242405	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.80[ASN][1000 genomes]
rs247423	0.90[ASN][1000 genomes]
rs247424	0.88[ASN][1000 genomes]
rs247425	0.89[ASN][1000 genomes]
rs247427	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs247431	0.94[ASN][1000 genomes]
rs247434	0.93[ASN][1000 genomes]
rs247436	0.94[ASN][1000 genomes]
rs247437	0.92[ASN][1000 genomes]
rs247438	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs247443	0.80[ASN][1000 genomes]
rs247447	0.82[JPT][hapmap]
rs2865527	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2865530	0.83[JPT][hapmap]
rs2865531	0.82[JPT][hapmap]
rs2865532	0.96[ASN][1000 genomes]
rs2903033	0.82[JPT][hapmap]
rs35263058	0.83[JPT][hapmap]
rs3743606	0.89[ASN][1000 genomes]
rs37602	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs3784936	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3784937	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3844219	0.96[ASN][1000 genomes]
rs3851733	0.83[JPT][hapmap]
rs3851735	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3851736	0.95[ASN][1000 genomes]
rs3851739	0.84[ASN][1000 genomes]
rs3863442	0.81[ASN][1000 genomes]
rs3863445	0.82[JPT][hapmap]
rs40217	0.82[ASN][1000 genomes]
rs4146809	0.83[JPT][hapmap]
rs4146810	0.82[JPT][hapmap]
rs42472	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4536500	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs455407	0.94[ASN][1000 genomes]
rs4638613	0.83[JPT][hapmap]
rs467223	0.93[ASN][1000 genomes]
rs467780	0.93[ASN][1000 genomes]
rs468079	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4887812	0.81[ASN][1000 genomes]
rs4887813	0.90[ASN][1000 genomes]
rs4887814	0.92[ASN][1000 genomes]
rs4887818	0.81[ASN][1000 genomes]
rs4887823	0.82[JPT][hapmap]
rs4887824	0.83[JPT][hapmap]
rs4887828	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs4888370	0.82[ASN][1000 genomes]
rs4888371	0.81[ASN][1000 genomes]
rs4888374	0.91[ASN][1000 genomes]
rs4888375	0.91[ASN][1000 genomes]
rs4888379	0.83[JPT][hapmap]
rs4888380	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4888381	0.99[ASN][1000 genomes]
rs4888383	0.83[JPT][hapmap]
rs4888386	0.83[JPT][hapmap]
rs4888387	0.82[JPT][hapmap]
rs4888388	0.83[JPT][hapmap]
rs4888389	0.83[JPT][hapmap]
rs4888393	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4888394	0.92[ASN][1000 genomes]
rs4888395	0.92[ASN][1000 genomes]
rs4888396	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4888397	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4888398	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4888405	0.83[JPT][hapmap]
rs4888415	0.82[JPT][hapmap]
rs4888416	0.83[JPT][hapmap]
rs4993971	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6564245	0.81[ASN][1000 genomes]
rs6564249	0.98[ASN][1000 genomes]
rs6564256	0.90[ASN][1000 genomes]
rs7187263	0.81[ASN][1000 genomes]
rs7188604	0.83[JPT][hapmap]
rs7189407	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7192155	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7194129	0.80[ASN][1000 genomes]
rs7199132	0.81[JPT][hapmap]
rs7199680	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7201989	0.80[EUR][1000 genomes]
rs7202284	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7203157	0.83[JPT][hapmap]
rs766521	0.83[JPT][hapmap]
rs766522	0.94[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8046109	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs8046184	0.92[ASN][1000 genomes]
rs8046416	0.81[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap]
rs8046949	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8048677	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8048816	0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8049611	0.92[ASN][1000 genomes]
rs8050059	0.83[JPT][hapmap]
rs8050662	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8051611	0.95[ASN][1000 genomes]
rs8051785	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8053632	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8054586	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8055609	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs889446	1.00[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9933956	0.99[ASN][1000 genomes]
rs9934007	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9989421	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1017239	CFDP1	cis	parietal	SCAN
rs1017239	RFWD3	cis	cerebellum	SCAN
rs1017239	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75338800-75426400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr16:75339400-75411800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr16:75340400-75374800	Weak transcription	Aorta	Aorta
4	chr16:75340800-75373400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr16:75341800-75364600	Weak transcription	Hela-S3	cervix
6	chr16:75342200-75381200	Weak transcription	Esophagus	oesophagus
7	chr16:75344000-75376400	Weak transcription	Gastric	stomach
8	chr16:75344600-75361400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr16:75344800-75359000	Weak transcription	Psoas Muscle	Psoas
10	chr16:75347600-75366000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr16:75348400-75374200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:75351600-75363200	Weak transcription	HepG2	liver
13	chr16:75352000-75361200	Weak transcription	Fetal Stomach	stomach
14	chr16:75352000-75368000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr16:75352200-75362600	Weak transcription	Fetal Intestine Large	intestine
16	chr16:75352200-75376400	Weak transcription	Pancreas	Pancrea
17	chr16:75352200-75396000	Weak transcription	Lung	lung
18	chr16:75354600-75358400	Enhancers	HMEC	breast
19	chr16:75354600-75362800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr16:75354600-75367800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr16:75354600-75373400	Weak transcription	Left Ventricle	heart
22	chr16:75354600-75375000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr16:75354800-75358400	Enhancers	NH-A	brain
24	chr16:75354800-75360200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr16:75354800-75363600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr16:75354800-75370800	Weak transcription	Brain Anterior Caudate	brain
27	chr16:75354800-75372400	Weak transcription	Fetal Lung	lung
28	chr16:75354800-75374800	Weak transcription	Liver	Liver
29	chr16:75354800-75413600	Weak transcription	Fetal Thymus	thymus
30	chr16:75355000-75359600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr16:75355000-75359600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr16:75355000-75359600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr16:75355000-75360200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr16:75355000-75364400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr16:75355000-75364600	Weak transcription	Brain Hippocampus Middle	brain
36	chr16:75355000-75368000	Weak transcription	Fetal Muscle Leg	muscle
37	chr16:75355000-75374600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr16:75355200-75360000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr16:75355200-75360000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr16:75355400-75360000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr16:75355400-75375000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr16:75355400-75379800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr16:75355600-75358800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr16:75355600-75359400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr16:75355600-75359800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr16:75355600-75360000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr16:75355600-75367600	Weak transcription	HSMMtube	muscle
48	chr16:75356400-75359200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr16:75356600-75359400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr16:75356600-75359400	Weak transcription	Fetal Heart	heart

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