Variant report

Variant	rs1919552
Chromosome Location	chr3:121469417-121469418
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	RFX5	chr3:121469315-121469515	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:121467550-121469430	GM12878	blood:	n/a	n/a
3	USF2	chr3:121468595-121469564	Hela-S3	cervix:	n/a	n/a
4	GTF2F1	chr3:121467982-121469471	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr3:121467777-121469634	IMR90	lung:	n/a	chr3:121468654-121468669
6	GABPA	chr3:121467798-121469571	A549	lung:	n/a	n/a
7	RFX5	chr3:121467515-121469850	SK-N-SH	brain:	n/a	chr3:121468710-121468719 chr3:121468652-121468669 chr3:121468653-121468668 chr3:121468629-121468638 chr3:121468653-121468668
8	REST	chr3:121467586-121469606	H1-neurons	neurons:	n/a	chr3:121468393-121468406 chr3:121468400-121468410
9	WRNIP1	chr3:121468252-121469463	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:121467036-121469449	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:121467771-121469447	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:121467293-121469486	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:121466284-121469653	IMR90	lung:	n/a	n/a
14	RFX5	chr3:121467360-121469816	IMR90	lung:	n/a	chr3:121468710-121468719 chr3:121468652-121468669 chr3:121468653-121468668 chr3:121468629-121468638 chr3:121468653-121468668
15	POLR2A	chr3:121467983-121469423	Raji	blood:	n/a	n/a
16	POLR2A	chr3:121466257-121469581	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr3:121466900-121469642	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:121468093-121469558	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:121467827-121469699	HepG2	liver:	n/a	n/a
20	GABPA	chr3:121467746-121469576	MCF-7	breast:	n/a	n/a
21	POLR2A	chr3:121466038-121469751	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr3:121467877-121469673	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:121468824..121470576-chr3:121473102..121475078,2	K562	blood:
2	chr3:121442817..121449533-chr3:121463247..121470201,7	K562	blood:
3	chr3:121465631..121470383-chr3:122100201..122104501,4	MCF-7	breast:
4	chr3:121468842..121470508-chr3:121478422..121481372,2	MCF-7	breast:
5	chr3:121469093..121470860-chr3:121480115..121482218,2	K562	blood:
6	chr3:121263260..121265570-chr3:121468289..121470216,2	K562	blood:
7	chr3:121449263..121451677-chr3:121468938..121471042,2	K562	blood:
8	chr3:121457664..121460185-chr3:121469014..121471399,2	MCF-7	breast:
9	chr3:121261975..121264944-chr3:121467360..121470216,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EAF2-3	chr3:121468132-121470030	NONHSAT091480

Variant related genes	Relation type
GOLGB1	TF binding region
ENSG00000114023	Chromatin interaction
ENSG00000051341	Chromatin interaction
ENSG00000173230	Chromatin interaction
ENSG00000160124	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10934560	0.82[EUR][1000 genomes]
rs12489511	1.00[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs12490565	0.95[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12631824	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13067629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1492177	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1574655	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1574735	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17849995	0.83[EUR][1000 genomes]
rs1873645	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs1919557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1986351	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1986874	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2001390	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001391	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070179	0.81[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes]
rs2332056	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap]
rs2840143	0.95[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs35295338	0.82[EUR][1000 genomes]
rs35713885	0.82[EUR][1000 genomes]
rs36022362	0.82[EUR][1000 genomes]
rs3772127	0.91[EUR][1000 genomes]
rs4676684	0.87[EUR][1000 genomes]
rs4676685	0.89[EUR][1000 genomes]
rs4676686	0.88[EUR][1000 genomes]
rs4676690	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4676751	0.81[EUR][1000 genomes]
rs57420306	0.82[EUR][1000 genomes]
rs59740137	0.83[EUR][1000 genomes]
rs6438645	0.91[EUR][1000 genomes]
rs6438660	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs6770719	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs6774164	0.82[EUR][1000 genomes]
rs6776703	0.81[EUR][1000 genomes]
rs6791896	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6792659	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6794341	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794677	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6802033	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes]
rs6803839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6807711	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73179983	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7375038	0.81[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7429247	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7430165	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611913	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs7620842	0.91[EUR][1000 genomes]
rs7646346	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs7646585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289172	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes]
rs9289173	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs9681209	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs9809114	0.81[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes]
rs9812411	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9829053	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9832267	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9835182	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854052	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9861992	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9864907	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9876021	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1919552	HCLS1	Cis_1M	lymphoblastoid	RTeQTL
rs1919552	SLC15A2	cis	cerebellum	SCAN
rs1919552	SLC15A2	cis	parietal	SCAN
rs1919552	ADPRH	cis	parietal	SCAN
rs1919552	PTPLB	cis	cerebellum	SCAN
rs1919552	MUC13	cis	cerebellum	SCAN
rs1919552	HCLS1	cis	Lymphoblastoid	GTEx
rs1919552	HCLS1	cis	lymphoblastoid	seeQTL
rs1919552	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs1919552	HCLS1	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121466400-121469600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:121466400-121469600	Active TSS	Right Atrium	heart
3	chr3:121466800-121469600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:121466800-121469600	Active TSS	Psoas Muscle	Psoas
5	chr3:121466800-121469800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:121466800-121469800	Active TSS	K562	blood
7	chr3:121467000-121469800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:121467000-121469800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr3:121467000-121469800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:121467000-121469800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:121467000-121469800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:121467200-121469800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:121467400-121469600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:121467400-121469600	Active TSS	Esophagus	oesophagus
15	chr3:121467400-121469600	Active TSS	Left Ventricle	heart
16	chr3:121467400-121469800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr3:121467400-121469800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:121467600-121469600	Active TSS	Colonic Mucosa	Colon
19	chr3:121467600-121469800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:121467600-121469800	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr3:121467800-121469600	Active TSS	Rectal Smooth Muscle	rectum
22	chr3:121468800-121469600	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr3:121468800-121469600	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr3:121468800-121469600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr3:121468800-121469600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:121468800-121469800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:121469000-121469600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr3:121469000-121469600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr3:121469000-121469600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:121469000-121469600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr3:121469000-121469600	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr3:121469000-121469600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr3:121469000-121469600	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr3:121469000-121469600	Flanking Active TSS	HUVEC	blood vessel
35	chr3:121469000-121469800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr3:121469000-121469800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr3:121469000-121469800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:121469000-121469800	Flanking Active TSS	Liver	Liver
39	chr3:121469000-121469800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr3:121469000-121469800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr3:121469200-121469600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:121469200-121469600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:121469200-121469600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr3:121469200-121469600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:121469200-121469600	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr3:121469200-121469600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr3:121469200-121469600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr3:121469200-121469600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:121469200-121469600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:121469200-121469600	Flanking Active TSS	Brain Angular Gyrus	brain

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