Variant report

Variant	rs3101747
Chromosome Location	chr19:38146386-38146387
allele	C/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	NRF1	chr19:38146079-38146920	Hela-S3	cervix:	n/a	chr19:38146748-38146762 chr19:38146696-38146705 chr19:38146751-38146765 chr19:38146402-38146411 chr19:38146751-38146760 chr19:38146750-38146761 chr19:38146758-38146767 chr19:38146751-38146762
2	POLR2A	chr19:38146106-38146590	K562	blood:	n/a	n/a
3	POLR2A	chr19:38145722-38146625	A549	lung:	n/a	n/a
4	POLR2A	chr19:38145479-38147391	HepG2	liver:	n/a	n/a
5	TAF1	chr19:38146163-38147341	H1-neurons	neurons:	n/a	n/a
6	ZMIZ1	chr19:38146017-38147202	K562	blood:	n/a	n/a
7	REST	chr19:38146105-38146466	PANC-1	pancreas:	n/a	chr19:38146308-38146321
8	TAF1	chr19:38145897-38147193	ECC-1	luminal epithelium:	n/a	n/a
9	EP300	chr19:38145610-38146611	A549	lung:	n/a	chr19:38146299-38146315 chr19:38146429-38146445
10	JUND	chr19:38145818-38146582	A549	lung:	n/a	chr19:38146408-38146417 chr19:38146241-38146255
11	ELF1	chr19:38146151-38146806	GM12878	blood:	n/a	n/a
12	YY1	chr19:38145590-38146658	GM12878	blood:	n/a	n/a
13	CHD2	chr19:38145886-38147414	K562	blood:	n/a	chr19:38146694-38146704
14	MAX	chr19:38145396-38147330	MCF-7	breast:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
15	FOS	chr19:38146314-38146417	MCF10A-Er-Src	breast:	n/a	chr19:38146408-38146417
16	POLR2A	chr19:38146093-38147229	HepG2	liver:	n/a	n/a
17	UBTF	chr19:38145350-38147258	K562	blood:	n/a	n/a
18	MAX	chr19:38145158-38147468	A549	lung:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
19	POLR2A	chr19:38145570-38147379	HL-60	blood:	n/a	n/a
20	E2F6	chr19:38145832-38147266	K562	blood:	n/a	chr19:38147005-38147014 chr19:38146696-38146705 chr19:38146752-38146761
21	USF1	chr19:38146335-38146534	HepG2	liver:	n/a	chr19:38146433-38146449
22	POLR2A	chr19:38145969-38147172	A549	lung:	n/a	n/a
23	POLR2A	chr19:38145482-38146938	Hela-S3	cervix:	n/a	n/a
24	GATA2	chr19:38145898-38147392	SH-SY5Y	brain:	n/a	n/a
25	TAF1	chr19:38145639-38147300	HepG2	liver:	n/a	n/a
26	UBTF	chr19:38145491-38147030	K562	blood:	n/a	n/a
27	USF1	chr19:38146324-38146549	SK-N-SH_RA	brain:	n/a	chr19:38146433-38146449
28	TAF1	chr19:38146139-38146490	Hela-S3	cervix:	n/a	n/a
29	BHLHE40	chr19:38146164-38147269	HepG2	liver:	n/a	chr19:38146433-38146449 chr19:38146999-38147015
30	CHD2	chr19:38146063-38147264	HepG2	liver:	n/a	chr19:38146694-38146704
31	CEBPB	chr19:38146031-38147033	Hela-S3	cervix:	n/a	n/a
32	REST	chr19:38146104-38147547	H1-neurons	neurons:	n/a	chr19:38146308-38146321 chr19:38146695-38146708
33	POLR2A	chr19:38146006-38146856	K562	blood:	n/a	n/a
34	ZKSCAN1	chr19:38145626-38147205	Hela-S3	cervix:	n/a	chr19:38146327-38146340
35	RAD21	chr19:38146233-38146550	SK-N-SH_RA	brain:	n/a	n/a
36	BHLHE40	chr19:38145729-38147344	K562	blood:	n/a	chr19:38146433-38146449 chr19:38146999-38147015
37	NRF1	chr19:38145869-38147564	SK-N-SH	brain:	n/a	chr19:38146748-38146762 chr19:38146696-38146705 chr19:38146751-38146765 chr19:38146402-38146411 chr19:38146751-38146760 chr19:38146750-38146761 chr19:38146758-38146767 chr19:38146751-38146762 chr19:38147005-38147014
38	POLR2A	chr19:38145510-38147461	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr19:38145590-38147291	MCF-7	breast:	n/a	n/a
40	TBP	chr19:38146081-38147264	HepG2	liver:	n/a	n/a
41	MAZ	chr19:38145365-38147377	IMR90	lung:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
42	POLR2A	chr19:38146142-38147177	HEK293	kidney:	n/a	n/a
43	MAX	chr19:38145131-38147074	Hela-S3	cervix:	n/a	chr19:38146453-38146462 chr19:38146550-38146559
44	POLR2A	chr19:38145503-38147263	GM12891	blood:	n/a	n/a
45	YY1	chr19:38145964-38147139	GM12878	blood:	n/a	chr19:38146696-38146705 chr19:38146683-38146697
46	TAF1	chr19:38146249-38146425	GM12892	blood:	n/a	n/a
47	POLR2A	chr19:38145503-38147000	Raji	blood:	n/a	n/a
48	MAX	chr19:38146129-38147183	K562	blood:	n/a	chr19:38146453-38146462 chr19:38146550-38146559
49	POLR2A	chr19:38145590-38147197	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:38145572-38147031	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75932176..75933046-chr19:38146017..38146882,2	Hela-S3	cervix:
2	chr19:38145174..38146985-chr19:38184008..38186251,2	MCF-7	breast:
3	chr19:38085961..38087829-chr19:38145172..38147580,2	K562	blood:
4	chr19:37957663..37960695-chr19:38143642..38147199,3	MCF-7	breast:
5	chr19:37958940..37961916-chr19:38146231..38147953,2	K562	blood:
6	chr19:37960304..37962188-chr19:38144303..38146867,2	MCF-7	breast:

Variant related genes	Relation type
ZFP30	TF binding region
ENSG00000177971	Chromatin interaction
ENSG00000267319	Chromatin interaction
ENSG00000196437	Chromatin interaction
ENSG00000171817	Chromatin interaction
ENSG00000171827	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10402671	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10403173	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10404031	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10406379	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10408619	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10409605	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10410588	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10412510	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10412786	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10417576	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420268	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10420552	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10425795	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11083432	0.95[EUR][1000 genomes]
rs11673023	0.83[EUR][1000 genomes]
rs12459015	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1291	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12974225	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12979640	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13744	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1531549	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1564206	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1564208	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16958861	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16958863	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1974714	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1975937	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1975939	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2075284	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287229	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291002	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2385119	0.81[ASN][1000 genomes]
rs28512414	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2909085	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2909088	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2909093	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2909098	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2909100	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2909102	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2909105	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2909109	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2927739	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2927740	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2927742	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2927746	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2927747	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972430	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972434	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972437	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972438	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972439	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972445	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972446	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972447	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972448	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2972452	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972458	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3095726	0.84[ASN][1000 genomes]
rs3101746	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3112433	0.91[ASN][1000 genomes]
rs3112434	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35863684	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829688	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802024	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802029	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803215	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4803231	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803233	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4803262	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803263	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803276	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803287	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56151076	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56317671	0.83[EUR][1000 genomes]
rs62108337	0.86[EUR][1000 genomes]
rs6508736	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8100646	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8103633	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8103647	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8110865	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs856300	0.80[ASN][1000 genomes]
rs9304568	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs954504	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs958305	0.93[EUR][1000 genomes]
rs968073	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9749368	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9797618	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9941475	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3101747	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38144000-38148000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:38144200-38147200	Active TSS	GM12878-XiMat	blood
3	chr19:38144400-38147600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38144600-38146800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:38144600-38147000	Active TSS	A549	lung
6	chr19:38144600-38147200	Active TSS	Fetal Kidney	kidney
7	chr19:38144600-38147400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:38144600-38147400	Active TSS	NHDF-Ad	bronchial
9	chr19:38144600-38147600	Active TSS	Fetal Stomach	stomach
10	chr19:38144600-38147600	Active TSS	Hela-S3	cervix
11	chr19:38144600-38147600	Active TSS	NHLF	lung
12	chr19:38144800-38146600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:38144800-38147200	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr19:38144800-38147200	Active TSS	Fetal Thymus	thymus
15	chr19:38144800-38147400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:38144800-38147400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:38144800-38147400	Active TSS	Left Ventricle	heart
18	chr19:38144800-38147600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr19:38144800-38147600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr19:38144800-38147600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:38144800-38147600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:38144800-38147600	Active TSS	Fetal Muscle Trunk	muscle
23	chr19:38145000-38147000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:38145000-38147000	Active TSS	Right Ventricle	heart
25	chr19:38145000-38147000	Active TSS	Stomach Smooth Muscle	stomach
26	chr19:38145000-38147200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:38145000-38147200	Active TSS	Muscle Satellite Cultured Cells	--
28	chr19:38145000-38147200	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr19:38145000-38147200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:38145000-38147200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:38145000-38147400	Active TSS	Ovary	ovary
32	chr19:38145000-38147400	Active TSS	Right Atrium	heart
33	chr19:38145000-38147600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr19:38145000-38147600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr19:38145000-38147600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:38145000-38147600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:38145000-38147600	Active TSS	Fetal Intestine Large	intestine
38	chr19:38145000-38147600	Active TSS	Psoas Muscle	Psoas
39	chr19:38145000-38147600	Active TSS	HSMM	muscle
40	chr19:38145000-38147600	Active TSS	HSMMtube	muscle
41	chr19:38145000-38147800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:38145200-38147000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:38145200-38147000	Active TSS	Placenta	Placenta
44	chr19:38145200-38147200	Active TSS	Colon Smooth Muscle	Colon
45	chr19:38145200-38147200	Active TSS	Fetal Lung	lung
46	chr19:38145200-38147200	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr19:38145200-38147200	Active TSS	Thymus	Thymus
48	chr19:38145200-38147200	Active TSS	Dnd41	blood
49	chr19:38145200-38147200	Active TSS	NHEK	skin
50	chr19:38145200-38147400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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