Variant report

Variant	rs11622731
Chromosome Location	chr14:39576570-39576571
allele	A/G
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	RAD21	chr14:39576564-39577217	SK-N-SH	brain:	n/a	chr14:39576932-39576951
2	CTCF	chr14:39576417-39577386	A549	lung:	n/a	chr14:39576931-39576949 chr14:39576933-39576954 chr14:39576934-39576947 chr14:39576932-39576948
3	RAD21	chr14:39576509-39577318	HepG2	liver:	n/a	chr14:39576932-39576951
4	TEAD4	chr14:39576234-39577308	HepG2	liver:	n/a	n/a
5	RAD21	chr14:39576565-39577215	HCT-116	colon:	n/a	chr14:39576932-39576951
6	CTCF	chr14:39576480-39576630	AG09319	gingival:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:39571044..39574449-chr14:39575206..39581914,9	K562	blood:
2	chr14:39569997..39574883-chr14:39575393..39578347,7	MCF-7	breast:
3	chr14:39572308..39574521-chr14:39576459..39578520,2	MCF-7	breast:
4	chr14:39576445..39577337-chr14:39837299..39838237,4	MCF-7	breast:
5	chr14:39576496..39577290-chr14:39837297..39837967,2	K562	blood:
6	chr14:39570753..39574803-chr14:39575206..39579488,6	K562	blood:

Variant related genes	Relation type
SEC23A	TF binding region
ENSG00000258591	TF binding region
ENSG00000100934	Chromatin interaction
ENSG00000258651	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1002193	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10129762	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10131369	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10134166	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10134656	0.82[AMR][1000 genomes]
rs10135561	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10136637	0.82[ASN][1000 genomes]
rs10140763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10141079	0.82[AMR][1000 genomes]
rs10141081	0.82[AMR][1000 genomes]
rs10141924	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10142117	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10142350	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10145417	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10145476	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10146176	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10148712	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10150756	0.82[AMR][1000 genomes]
rs10151124	0.83[AMR][1000 genomes]
rs10483542	0.82[JPT][hapmap]
rs10483543	0.88[CEU][hapmap];0.91[AMR][1000 genomes]
rs1050136	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs11622968	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11623907	0.82[AMR][1000 genomes]
rs11623945	0.82[AMR][1000 genomes]
rs11624584	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11625689	0.82[AMR][1000 genomes]
rs11626002	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11627264	0.82[AMR][1000 genomes]
rs11628564	0.82[AMR][1000 genomes]
rs11628784	0.88[CEU][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11845793	0.82[AMR][1000 genomes]
rs11848067	0.82[AMR][1000 genomes]
rs11849209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11850579	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11851680	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12323565	0.82[AMR][1000 genomes]
rs12587208	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13379129	0.84[ASN][1000 genomes]
rs17092044	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17092050	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17108596	0.82[AMR][1000 genomes]
rs17108696	0.82[AMR][1000 genomes]
rs17108948	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2025061	0.82[AMR][1000 genomes]
rs2144528	0.82[AMR][1000 genomes]
rs2144530	0.81[ASN][1000 genomes]
rs2273592	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2277458	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs28414518	0.82[AMR][1000 genomes]
rs28437577	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28470602	0.82[AMR][1000 genomes]
rs28501673	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28583114	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28666016	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28821293	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759544	0.82[JPT][hapmap]
rs45622837	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55672305	0.82[AMR][1000 genomes]
rs55737943	0.82[AMR][1000 genomes]
rs56064304	0.82[AMR][1000 genomes]
rs56105133	0.82[AMR][1000 genomes]
rs57326310	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57482489	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57555422	0.84[ASN][1000 genomes]
rs58601678	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59465524	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7144625	0.82[AMR][1000 genomes]
rs7155307	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7156264	0.81[CHB][hapmap];0.82[YRI][hapmap]
rs7159520	0.82[AMR][1000 genomes]
rs74048710	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74048711	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761805	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8018720	0.85[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs8019396	0.82[AMR][1000 genomes]
rs926970	0.82[AMR][1000 genomes]
rs926971	0.82[JPT][hapmap]
rs993675	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11622731	PNN	cis	lymphoblastoid	seeQTL
rs11622731	BRMS1L	cis	cerebellum	SCAN
rs11622731	CTAGE5	cis	parietal	SCAN
rs11622731	EAPP	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39573200-39577800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:39573400-39578800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr14:39573400-39579000	Weak transcription	K562	blood
4	chr14:39573400-39582400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:39573400-39583000	Weak transcription	HSMM	muscle
6	chr14:39573800-39583000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr14:39573800-39583000	Weak transcription	Thymus	Thymus
8	chr14:39574000-39576600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:39574000-39582400	Weak transcription	A549	lung
10	chr14:39574000-39582800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr14:39574000-39583000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr14:39574000-39583000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr14:39574000-39583000	Weak transcription	Stomach Mucosa	stomach
14	chr14:39574200-39576800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr14:39574200-39582400	Weak transcription	Dnd41	blood
16	chr14:39574200-39583000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr14:39574400-39576800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr14:39574400-39576800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr14:39574400-39578400	Weak transcription	GM12878-XiMat	blood
20	chr14:39574400-39582400	Weak transcription	Hela-S3	cervix
21	chr14:39574400-39582800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr14:39576200-39576600	Enhancers	Fetal Intestine Small	intestine
23	chr14:39576400-39577200	Enhancers	Fetal Intestine Large	intestine
24	chr14:39576400-39578000	Enhancers	HepG2	liver

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