Variant report

Variant	rs73590568
Chromosome Location	chr19:36204542-36204543
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	MTA3	chr19:36203117-36208944	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:36203385-36212934	GM12892	blood:	n/a	n/a
3	RELA	chr19:36203418-36204555	GM18505	blood:	n/a	n/a
4	STAT5A	chr19:36203130-36204970	GM12878	blood:	n/a	chr19:36203432-36203443 chr19:36203458-36203470 chr19:36204460-36204472 chr19:36203739-36203751
5	TAF1	chr19:36204149-36204599	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:36204408-36204724	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr19:36203844-36205008	Raji	blood:	n/a	n/a
8	POLR2A	chr19:36203571-36204601	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:36202991-36212995	GM12878	blood:	n/a	n/a
10	WRNIP1	chr19:36203485-36205570	GM12878	blood:	n/a	n/a
11	SMC3	chr19:36203894-36204578	GM12878	blood:	n/a	n/a
12	POU2F2	chr19:36203398-36204619	GM12891	blood:	n/a	n/a
13	SIN3A	chr19:36203496-36204595	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:36203738-36204576	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:36203535-36204579	GM18505	blood:	n/a	n/a
16	POLR2A	chr19:36203492-36205805	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:36203737-36204571	GM18526	blood:	n/a	n/a
18	CREB1	chr19:36203273-36204625	GM12878	blood:	n/a	n/a
19	POU2F2	chr19:36203420-36204640	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:36203433-36204642	GM19099	blood:	n/a	n/a
21	POLR2A	chr19:36202895-36208735	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:36204000-36204575	GM12878	blood:	n/a	n/a
23	CHD1	chr19:36203464-36204920	GM12878	blood:	n/a	n/a
24	EBF1	chr19:36203310-36204545	GM12878	blood:	n/a	chr19:36203523-36203534
25	PAX5	chr19:36203422-36204633	GM12878	blood:	n/a	chr19:36203535-36203544 chr19:36203532-36203541
26	POLR2A	chr19:36203628-36204554	GM12892	blood:	n/a	n/a
27	BCLAF1	chr19:36203641-36204678	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:36203580-36208801	GM12891	blood:	n/a	n/a
29	IKZF1	chr19:36203463-36205250	GM12878	blood:	n/a	n/a
30	MAZ	chr19:36203408-36204852	GM12878	blood:	n/a	n/a
31	MXI1	chr19:36203558-36205262	GM12878	blood:	n/a	n/a
32	CUX1	chr19:36203396-36204614	GM12878	blood:	n/a	n/a
33	RELA	chr19:36203369-36204819	GM10847	blood:	n/a	n/a
34	TBP	chr19:36203361-36204582	GM12878	blood:	n/a	chr19:36203643-36203654
35	RCOR1	chr19:36203312-36204620	GM12878	blood:	n/a	n/a
36	RUNX3	chr19:36203389-36205352	GM12878	blood:	n/a	n/a
37	NFATC1	chr19:36203176-36204608	GM12878	blood:	n/a	n/a
38	RELA	chr19:36203396-36205049	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:36203634-36204589	GM15510	blood:	n/a	n/a
40	RELA	chr19:36203147-36204659	GM18951	blood:	n/a	n/a
41	STAT1	chr19:36203572-36205549	GM12878	blood:	n/a	chr19:36205399-36205411 chr19:36204460-36204472 chr19:36203739-36203751
42	POLR2A	chr19:36203522-36210520	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:36203532-36204610	GM12891	blood:	n/a	n/a
44	TAF1	chr19:36204049-36204594	GM12892	blood:	n/a	n/a
45	RUNX3	chr19:36203218-36204739	GM12878	blood:	n/a	n/a
46	TAF1	chr19:36203798-36204562	GM12878	blood:	n/a	n/a
47	POLR2A	chr19:36203650-36210832	GM12891	blood:	n/a	n/a
48	RELA	chr19:36203498-36204767	GM15510	blood:	n/a	n/a
49	EP300	chr19:36203223-36205157	GM12878	blood:	n/a	chr19:36205027-36205034 chr19:36203427-36203441 chr19:36203530-36203544 chr19:36203421-36203435
50	BCLAF1	chr19:36203597-36204677	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36203511..36205032-chr19:36208383..36210782,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272333	TF binding region
KMT2B	TF binding region
ENSG00000272333	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11546662	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11546665	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16970649	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17776834	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2227278	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234375	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267585	0.86[EUR][1000 genomes]
rs2267586	0.87[EUR][1000 genomes]
rs2285420	0.94[EUR][1000 genomes]
rs231217	0.83[AMR][1000 genomes]
rs2871893	0.84[EUR][1000 genomes]
rs2871894	0.84[EUR][1000 genomes]
rs34562867	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3817622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3893069	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4580318	0.86[EUR][1000 genomes]
rs4992668	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56849855	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57180990	0.86[EUR][1000 genomes]
rs58142685	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58255615	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58496446	0.86[EUR][1000 genomes]
rs58952294	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61254015	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61351824	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61375471	0.86[EUR][1000 genomes]
rs73590543	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590544	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73590559	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590561	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590564	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73590576	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590585	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73590591	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73590598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73592416	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73592448	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73592461	0.80[EUR][1000 genomes]
rs73599271	0.85[EUR][1000 genomes]
rs73599272	0.83[EUR][1000 genomes]
rs73599274	0.83[EUR][1000 genomes]
rs73599279	0.84[EUR][1000 genomes]
rs73599281	0.84[EUR][1000 genomes]
rs73599286	0.86[EUR][1000 genomes]
rs73599289	0.86[EUR][1000 genomes]
rs73600880	0.86[EUR][1000 genomes]
rs73600881	0.86[EUR][1000 genomes]
rs73600885	0.87[EUR][1000 genomes]
rs73600892	0.84[EUR][1000 genomes]
rs73600893	0.86[EUR][1000 genomes]
rs73600899	0.93[EUR][1000 genomes]
rs73602803	0.94[EUR][1000 genomes]
rs73602804	0.94[EUR][1000 genomes]
rs73602806	0.94[EUR][1000 genomes]
rs73602823	0.86[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs73602827	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73602832	0.99[EUR][1000 genomes]
rs73602833	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36194000-36206600	Weak transcription	Brain Angular Gyrus	brain
2	chr19:36194000-36206800	Weak transcription	Right Atrium	heart
3	chr19:36194000-36206800	Weak transcription	Osteobl	bone
4	chr19:36194600-36206200	Weak transcription	Right Ventricle	heart
5	chr19:36195400-36206600	Weak transcription	Gastric	stomach
6	chr19:36198000-36205400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr19:36201200-36206600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:36201200-36207000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr19:36201400-36206400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr19:36201600-36204800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:36201600-36206000	Enhancers	Spleen	Spleen
12	chr19:36201600-36207000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr19:36201600-36207200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:36201800-36206800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr19:36202000-36204600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:36202200-36206400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:36202200-36206400	Weak transcription	Brain Anterior Caudate	brain
18	chr19:36202200-36207000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr19:36202400-36206200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:36202400-36206400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr19:36202600-36205400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:36202600-36205600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:36202600-36205800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:36202600-36205800	Weak transcription	Colonic Mucosa	Colon
25	chr19:36202600-36206000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:36202600-36206200	Weak transcription	Esophagus	oesophagus
27	chr19:36202600-36206200	Weak transcription	A549	lung
28	chr19:36202600-36206400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:36202600-36206600	Weak transcription	NHEK	skin
30	chr19:36203200-36207400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr19:36203600-36204800	Enhancers	K562	blood
32	chr19:36203600-36207600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr19:36203800-36205800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr19:36204000-36204600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr19:36204000-36204600	Enhancers	H9 Cell Line	embryonic stem cell
36	chr19:36204000-36204600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:36204000-36205000	Enhancers	Fetal Thymus	thymus
38	chr19:36204000-36205400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
39	chr19:36204000-36206000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:36204000-36206000	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr19:36204000-36206400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:36204200-36204800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr19:36204200-36205000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:36204200-36205200	Active TSS	GM12878-XiMat	blood
45	chr19:36204200-36205200	Weak transcription	HepG2	liver
46	chr19:36204200-36206400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:36204200-36206600	Weak transcription	Small Intestine	intestine
48	chr19:36204400-36204800	Enhancers	Primary T cells from cord blood	blood
49	chr19:36204400-36205000	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr19:36204400-36205200	Active TSS	Rectal Smooth Muscle	rectum

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