Variant report

Variant	rs35729071
Chromosome Location	chr19:36204427-36204428
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	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	PBX3	chr19:36203993-36204441	GM12878	blood:	n/a	n/a
11	NFYB	chr19:36204036-36204471	GM12878	blood:	n/a	n/a
12	WRNIP1	chr19:36203485-36205570	GM12878	blood:	n/a	n/a
13	SMC3	chr19:36203894-36204578	GM12878	blood:	n/a	n/a
14	POU2F2	chr19:36203398-36204619	GM12891	blood:	n/a	n/a
15	SIN3A	chr19:36203496-36204595	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:36203738-36204576	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:36203535-36204579	GM18505	blood:	n/a	n/a
18	POLR2A	chr19:36203492-36205805	GM12892	blood:	n/a	n/a
19	POLR2A	chr19:36203737-36204571	GM18526	blood:	n/a	n/a
20	CREB1	chr19:36203273-36204625	GM12878	blood:	n/a	n/a
21	POU2F2	chr19:36203420-36204640	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:36203433-36204642	GM19099	blood:	n/a	n/a
23	ATF2	chr19:36203263-36204517	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:36202895-36208735	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:36204000-36204575	GM12878	blood:	n/a	n/a
26	CHD1	chr19:36203464-36204920	GM12878	blood:	n/a	n/a
27	EBF1	chr19:36203310-36204545	GM12878	blood:	n/a	chr19:36203523-36203534
28	PAX5	chr19:36203422-36204633	GM12878	blood:	n/a	chr19:36203535-36203544 chr19:36203532-36203541
29	POLR2A	chr19:36203628-36204554	GM12892	blood:	n/a	n/a
30	BCLAF1	chr19:36203641-36204678	GM12878	blood:	n/a	n/a
31	TAF1	chr19:36203955-36204534	GM12891	blood:	n/a	n/a
32	POLR2A	chr19:36203580-36208801	GM12891	blood:	n/a	n/a
33	IRF4	chr19:36203388-36204493	GM12878	blood:	n/a	n/a
34	SP1	chr19:36203426-36204535	GM12878	blood:	n/a	chr19:36203643-36203650 chr19:36204463-36204472 chr19:36203739-36203753
35	IKZF1	chr19:36203463-36205250	GM12878	blood:	n/a	n/a
36	NFIC	chr19:36203251-36204517	GM12878	blood:	n/a	n/a
37	MAZ	chr19:36203408-36204852	GM12878	blood:	n/a	n/a
38	MXI1	chr19:36203558-36205262	GM12878	blood:	n/a	n/a
39	ELK1	chr19:36203750-36204534	GM12878	blood:	n/a	n/a
40	CUX1	chr19:36203396-36204614	GM12878	blood:	n/a	n/a
41	TAF1	chr19:36203908-36204506	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:36203515-36204525	GM12891	blood:	n/a	n/a
43	RELA	chr19:36203369-36204819	GM10847	blood:	n/a	n/a
44	TBP	chr19:36203361-36204582	GM12878	blood:	n/a	chr19:36203643-36203654
45	RCOR1	chr19:36203312-36204620	GM12878	blood:	n/a	n/a
46	YY1	chr19:36204078-36204477	GM12892	blood:	n/a	n/a
47	POLR2A	chr19:36204404-36204526	Hela-S3	cervix:	n/a	n/a
48	RUNX3	chr19:36203389-36205352	GM12878	blood:	n/a	n/a
49	NFATC1	chr19:36203176-36204608	GM12878	blood:	n/a	n/a
50	RELA	chr19:36203396-36205049	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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB32-2	chr19:36203819-36204444	ENSG00000241762.1

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

Extended variants
information (count: 30 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10402837	0.82[EUR][1000 genomes]
rs10413852	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs12104249	0.88[EUR][1000 genomes]
rs12459073	0.81[EUR][1000 genomes]
rs12459634	0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.85[AFR][1000 genomes]
rs12461285	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12461333	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12463059	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2234371	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs230261	1.00[CHD][hapmap]
rs28633929	0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs28656784	0.80[EUR][1000 genomes]
rs2871921	0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs34031911	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35209304	0.92[EUR][1000 genomes]
rs3848662	0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs3848665	0.80[EUR][1000 genomes]
rs56189160	0.85[EUR][1000 genomes]
rs62109452	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62109998	0.91[EUR][1000 genomes]
rs7249885	0.97[EUR][1000 genomes]
rs73048504	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8106959	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs9304874	0.82[AMR][1000 genomes];0.98[EUR][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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs35729071	EIF3K	cis	parietal	SCAN
rs35729071	ZNF568	cis	cerebellum	SCAN
rs35729071	UPK1A	trans	cerebellum	SCAN
rs35729071	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs35729071	CNFN	cis	cerebellum	SCAN
rs35729071	RN7SL765P	cis	Muscle Skeletal	GTEx
rs35729071	U2AF1L4	cis	Muscle Skeletal	GTEx
rs35729071	PSG1	cis	parietal	SCAN
rs35729071	TMEM149	cis	lymphoblastoid	seeQTL
rs35729071	TMEM149	cis	multi-tissue	Pritchard
rs35729071	TMEM149	Cis_1M	lymphoblastoid	RTeQTL

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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