Variant report

Variant	rs7260610
Chromosome Location	chr19:40596802-40596803
allele	G/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	PML	chr19:40596103-40597172	K562	blood:	n/a	n/a
2	ATF2	chr19:40596328-40597044	GM12878	blood:	n/a	n/a
3	ZNF143	chr19:40596202-40597101	Hela-S3	cervix:	n/a	chr19:40596859-40596877 chr19:40596854-40596873
4	ELF1	chr19:40596617-40597007	HepG2	liver:	n/a	chr19:40596835-40596846 chr19:40596835-40596846 chr19:40596854-40596866
5	EP300	chr19:40596356-40596976	GM12878	blood:	n/a	chr19:40596838-40596845
6	POLR2A	chr19:40596088-40597179	HepG2	liver:	n/a	n/a
7	MYC	chr19:40596265-40596988	NB4	blood:	n/a	n/a
8	YY1	chr19:40596089-40597072	K562	blood:	n/a	n/a
9	POLR2A	chr19:40596151-40597173	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr19:40596031-40597187	H1-hESC	embryonic stem cell:	n/a	n/a
11	HEY1	chr19:40596244-40597160	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:40596492-40597123	HUVEC	blood vessel:	n/a	n/a
13	SMC3	chr19:40596340-40597127	Hela-S3	cervix:	n/a	n/a
14	FOSL2	chr19:40596072-40597598	A549	lung:	n/a	chr19:40596194-40596206
15	POLR2A	chr19:40596584-40597128	HCT-116	colon:	n/a	n/a
16	E2F6	chr19:40596779-40597072	K562	blood:	n/a	n/a
17	NFYB	chr19:40596780-40596819	GM12878	blood:	n/a	n/a
18	STAT1	chr19:40596527-40597126	GM12878	blood:	n/a	n/a
19	IRF1	chr19:40596192-40597169	K562	blood:	n/a	n/a
20	WRNIP1	chr19:40595947-40596992	GM12878	blood:	n/a	n/a
21	TEAD4	chr19:40595995-40597132	K562	blood:	n/a	n/a
22	UBTF	chr19:40596230-40597038	K562	blood:	n/a	n/a
23	RUNX3	chr19:40595945-40597114	GM12878	blood:	n/a	n/a
24	ELK4	chr19:40596159-40597090	Hela-S3	cervix:	n/a	chr19:40596837-40596846 chr19:40596836-40596847 chr19:40596837-40596845
25	TAF1	chr19:40596336-40597136	K562	blood:	n/a	n/a
26	POLR2A	chr19:40596167-40597161	K562	blood:	n/a	n/a
27	SIX5	chr19:40596605-40597003	GM12878	blood:	n/a	n/a
28	MXI1	chr19:40596279-40597112	K562	blood:	n/a	n/a
29	POLR2A	chr19:40596391-40597275	U87	brain:	n/a	n/a
30	CREB1	chr19:40596226-40597244	GM12878	blood:	n/a	n/a
31	CHD1	chr19:40596363-40596919	GM12878	blood:	n/a	n/a
32	REST	chr19:40596445-40597112	PFSK-1	brain:	n/a	chr19:40596456-40596474
33	ZMIZ1	chr19:40596309-40597077	K562	blood:	n/a	n/a
34	ELF1	chr19:40596547-40597076	HepG2	liver:	n/a	chr19:40596835-40596846 chr19:40596835-40596846 chr19:40596854-40596866
35	HDAC2	chr19:40596507-40597098	HepG2	liver:	n/a	chr19:40597074-40597088
36	PML	chr19:40596672-40597045	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:40596023-40597336	GM12878	blood:	n/a	n/a
38	HEY1	chr19:40596192-40597092	K562	blood:	n/a	n/a
39	SIN3AK20	chr19:40596050-40597288	MCF-7	breast:	n/a	n/a
40	MYC	chr19:40596423-40596851	MCF-7	breast:	n/a	n/a
41	POLR2A	chr19:40596316-40597080	GM12891	blood:	n/a	n/a
42	TAF1	chr19:40596634-40597105	Hela-S3	cervix:	n/a	n/a
43	MXI1	chr19:40596410-40596962	H1-hESC	embryonic stem cell:	n/a	n/a
44	CREB1	chr19:40596258-40597196	GM12878	blood:	n/a	n/a
45	CREB1	chr19:40596186-40597118	HepG2	liver:	n/a	n/a
46	POLR2A	chr19:40596400-40597072	H1-hESC	embryonic stem cell:	n/a	n/a
47	TAF1	chr19:40596362-40597149	GM12878	blood:	n/a	n/a
48	HCFC1	chr19:40595389-40597742	Hela-S3	cervix:	n/a	n/a
49	PML	chr19:40596500-40597124	K562	blood:	n/a	n/a
50	TAF1	chr19:40596327-40597070	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40501950..40503610-chr19:40595158..40598072,2	K562	blood:
2	chr13:91999624..92000352-chr19:40596463..40597085,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF546-3	chr19:40596661-40600313	ENSG00000269296.1

Variant related genes	Relation type
ZNF780A	TF binding region
ENSG00000187187	Chromatin interaction
ENSG00000215417	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10414087	1.00[ASN][1000 genomes]
rs10418532	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424773	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881677	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11882464	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882490	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163212	1.00[ASN][1000 genomes]
rs16973959	1.00[CHB][hapmap]
rs17756648	0.83[ASN][1000 genomes]
rs234329	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs234338	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs234347	1.00[CHB][hapmap]
rs234348	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs234359	0.85[YRI][hapmap]
rs234362	1.00[CHB][hapmap]
rs234363	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs234367	1.00[CHB][hapmap]
rs234369	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2531363	1.00[CHB][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2542311	0.86[YRI][hapmap]
rs28669038	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337796	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs383975	1.00[ASN][1000 genomes]
rs399405	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs420413	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs445379	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs517342	1.00[ASN][1000 genomes]
rs520877	1.00[ASN][1000 genomes]
rs526467	1.00[ASN][1000 genomes]
rs532235	1.00[ASN][1000 genomes]
rs563703	1.00[ASN][1000 genomes]
rs589279	1.00[ASN][1000 genomes]
rs589404	1.00[ASN][1000 genomes]
rs62106576	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106577	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106578	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106580	0.83[ASN][1000 genomes]
rs62106581	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62106584	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106585	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62106586	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106587	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106588	1.00[ASN][1000 genomes]
rs62106589	1.00[ASN][1000 genomes]
rs62106590	1.00[ASN][1000 genomes]
rs62106591	1.00[ASN][1000 genomes]
rs62106625	1.00[ASN][1000 genomes]
rs62106626	1.00[ASN][1000 genomes]
rs62108934	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110063	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623196	1.00[ASN][1000 genomes]
rs636313	1.00[ASN][1000 genomes]
rs649239	1.00[ASN][1000 genomes]
rs6508931	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508932	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667850	1.00[ASN][1000 genomes]
rs7250244	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250298	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259136	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73551672	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73553618	1.00[ASN][1000 genomes]
rs8103746	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103807	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104932	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8105260	1.00[ASN][1000 genomes]
rs8108062	1.00[ASN][1000 genomes]
rs8108857	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv2488	chr19:40593818-40631406	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40595200-40597400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr19:40595200-40597400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:40595400-40597000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:40595400-40597400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr19:40595400-40597400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:40595400-40597400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:40595400-40597400	Active TSS	Right Ventricle	heart
8	chr19:40595400-40597600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:40595400-40597600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:40595400-40597600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:40595400-40597600	Active TSS	Rectal Smooth Muscle	rectum
12	chr19:40595600-40597200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr19:40595600-40597200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:40595600-40597200	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr19:40595600-40597400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr19:40595600-40597400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:40595600-40597400	Active TSS	Aorta	Aorta
18	chr19:40595600-40597400	Active TSS	Fetal Intestine Small	intestine
19	chr19:40595600-40597400	Active TSS	Fetal Muscle Trunk	muscle
20	chr19:40595600-40597400	Active TSS	Psoas Muscle	Psoas
21	chr19:40595600-40597400	Active TSS	HSMM	muscle
22	chr19:40595600-40597600	Active TSS	Fetal Intestine Large	intestine
23	chr19:40595600-40597600	Active TSS	Fetal Kidney	kidney
24	chr19:40595800-40597200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr19:40595800-40597200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr19:40595800-40597200	Active TSS	Duodenum Mucosa	Duodenum
27	chr19:40595800-40597200	Active TSS	Esophagus	oesophagus
28	chr19:40595800-40597200	Active TSS	Gastric	stomach
29	chr19:40595800-40597200	Active TSS	Ovary	ovary
30	chr19:40595800-40597200	Active TSS	Thymus	Thymus
31	chr19:40595800-40597200	Active TSS	A549	lung
32	chr19:40595800-40597400	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr19:40595800-40597400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:40595800-40597400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:40595800-40597400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:40595800-40597400	Active TSS	Right Atrium	heart
37	chr19:40595800-40597400	Active TSS	K562	blood
38	chr19:40595800-40597600	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr19:40595800-40597600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:40595800-40597600	Active TSS	Colonic Mucosa	Colon
41	chr19:40595800-40597600	Active TSS	NHDF-Ad	bronchial
42	chr19:40595800-40597800	Active TSS	GM12878-XiMat	blood
43	chr19:40596000-40597000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:40596000-40597200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:40596000-40597200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:40596000-40597200	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr19:40596000-40597200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:40596000-40597200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr19:40596000-40597200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:40596000-40597200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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