Variant report

Variant	rs652429
Chromosome Location	chr11:107314877-107314878
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	JUN	chr11:107314724-107314899	K562	blood:	n/a	n/a

Variant related genes	Relation type
CWF19L2	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10444318	0.86[EUR][1000 genomes]
rs11212134	0.85[EUR][1000 genomes]
rs11212148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs11212174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs11212199	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11212238	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12361977	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12363600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs12364307	0.90[EUR][1000 genomes]
rs12365270	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1263297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1272372	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12796588	0.85[EUR][1000 genomes]
rs12800923	1.00[CHB][hapmap]
rs17587706	1.00[CHB][hapmap]
rs2432867	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34129089	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34443916	0.90[EUR][1000 genomes]
rs34661012	0.89[EUR][1000 genomes]
rs34846704	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34938694	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35468021	0.82[EUR][1000 genomes]
rs35504279	0.86[EUR][1000 genomes]
rs476028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs480609	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs487705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs504617	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs510528	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs514117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs517734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs517929	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs518580	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs524764	0.80[TSI][hapmap]
rs526875	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs527801	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs528337	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs529341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs536636	1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs537563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs541782	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs546313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs548049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs549909	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs554506	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs570235	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs584778	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs588678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs589415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59590014	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs596268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs599677	1.00[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs602625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs608352	0.82[EUR][1000 genomes]
rs612080	1.00[CHB][hapmap]
rs618078	0.80[TSI][hapmap]
rs619933	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs626091	1.00[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs627440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs628609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs629755	0.82[EUR][1000 genomes]
rs632186	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs632910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs632942	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs633543	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs644954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs649331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs654272	0.80[TSI][hapmap]
rs659040	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs661085	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs664836	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs667198	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs668415	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67052454	0.86[EUR][1000 genomes]
rs673267	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67428239	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs675081	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68000908	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs68027391	0.84[EUR][1000 genomes]
rs7129866	0.90[EUR][1000 genomes]
rs784147	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs784149	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7924335	1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898365	chr11:106944975-107430300	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv898366	chr11:106944975-107433835	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv898367	chr11:106944975-107443420	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv898369	chr11:106958304-107443420	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv898370	chr11:107027991-107430300	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv898372	chr11:107049968-107433835	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1038368	chr11:107116577-107664181	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv541163	chr11:107116577-107664181	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv898373	chr11:107124903-107433835	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv832261	chr11:107145901-107321562	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv2756363	chr11:107189790-107376790	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv556376	chr11:107250851-107486598	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv898375	chr11:107299631-107365191	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv898376	chr11:107299631-107443420	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs652429	CWF19L2	cis	multi-tissue	Pritchard
rs652429	CWF19L2	cis	parietal	SCAN
rs652429	CWF19L2	Cis_1M	lymphoblastoid	RTeQTL
rs652429	GUCY1A2	cis	cerebellum	SCAN
rs652429	CWF19L2	cis	Artery Tibial	GTEx
rs652429	CWF19L2	cis	cerebellum	SCAN
rs652429	CWF19L2	cis	Liver	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107241600-107327800	Weak transcription	HSMMtube	muscle
2	chr11:107252600-107323800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:107255000-107327600	Weak transcription	Fetal Heart	heart
4	chr11:107256600-107327600	Weak transcription	NHDF-Ad	bronchial
5	chr11:107258800-107324200	Weak transcription	Small Intestine	intestine
6	chr11:107259600-107323400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:107262200-107324000	Weak transcription	Pancreas	Pancrea
8	chr11:107268600-107323400	Weak transcription	Gastric	stomach
9	chr11:107269000-107324600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:107274600-107323400	Weak transcription	Esophagus	oesophagus
11	chr11:107286600-107322800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr11:107291400-107324000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:107292800-107327600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:107294200-107317800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:107296400-107323600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:107296800-107325600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr11:107297200-107324400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:107298200-107327400	Weak transcription	A549	lung
19	chr11:107300200-107323200	Weak transcription	HSMM	muscle
20	chr11:107300400-107324200	Weak transcription	NHLF	lung
21	chr11:107300400-107326800	Weak transcription	Hela-S3	cervix
22	chr11:107301000-107326800	Weak transcription	HMEC	breast
23	chr11:107305000-107319600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:107306800-107318200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:107307000-107318800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr11:107307000-107319400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:107307400-107315800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:107307400-107323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:107307400-107323400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:107307600-107323200	Weak transcription	Osteobl	bone
31	chr11:107307800-107323400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:107307800-107323400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:107307800-107326800	Weak transcription	Fetal Brain Male	brain
34	chr11:107308000-107317200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr11:107308000-107319600	Strong transcription	Adipose Nuclei	Adipose
36	chr11:107308200-107315400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:107308200-107316200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:107308200-107317600	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr11:107308200-107318400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:107308200-107319600	Strong transcription	Primary T cells from cord blood	blood
41	chr11:107308200-107319600	Strong transcription	Fetal Thymus	thymus
42	chr11:107308400-107319600	Strong transcription	Primary B cells from cord blood	blood
43	chr11:107308400-107319600	Strong transcription	Liver	Liver
44	chr11:107308600-107317800	Strong transcription	Fetal Intestine Large	intestine
45	chr11:107308800-107315600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:107308800-107315800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr11:107308800-107318800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr11:107309000-107317200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr11:107309200-107324000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:107309400-107315200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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