Variant report

Variant	rs2234360
Chromosome Location	chr19:36203044-36203045
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	POLR2A	chr19:36202991-36212995	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:36202895-36208735	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:36202912-36211124	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:36202882-36208827	GM12892	blood:	n/a	n/a
5	PML	chr19:36202992-36204739	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36201857..36203426-chr19:36205188..36208060,2	MCF-7	breast:
2	chr19:35763154..35765323-chr19:36201276..36203802,2	K562	blood:

Variant related genes	Relation type
ZBTB32	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

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]
rs11882996	0.80[ASW][hapmap]
rs16970649	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[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	0.88[CEU][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs2285420	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];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[CHB][hapmap];0.82[YRI][hapmap];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]
rs73590568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:7 , 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	nsv543995	chr19:36139204-36203592	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2234360	DPF1	cis	parietal	SCAN
rs2234360	PLD3	cis	cerebellum	SCAN
rs2234360	TEX101	cis	parietal	SCAN

Chromatin state (count:44 , 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	chr19:36199400-36204000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:36200400-36203200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr19:36200400-36204000	Enhancers	Primary B cells from peripheral blood	blood
10	chr19:36201000-36204000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:36201200-36206600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:36201200-36207000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr19:36201400-36204200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:36201400-36206400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr19:36201600-36204800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:36201600-36206000	Enhancers	Spleen	Spleen
17	chr19:36201600-36207000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr19:36201600-36207200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:36201800-36206800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr19:36202000-36204600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:36202200-36204200	Enhancers	Primary T cells fromperipheralblood	blood
22	chr19:36202200-36204200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:36202200-36206400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:36202200-36206400	Weak transcription	Brain Anterior Caudate	brain
25	chr19:36202200-36207000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr19:36202400-36203600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr19:36202400-36204000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:36202400-36204000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr19:36202400-36206200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:36202400-36206400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:36202600-36203200	Enhancers	GM12878-XiMat	blood
32	chr19:36202600-36203800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:36202600-36204000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:36202600-36205400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr19:36202600-36205600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:36202600-36205800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:36202600-36205800	Weak transcription	Colonic Mucosa	Colon
38	chr19:36202600-36206000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr19:36202600-36206200	Weak transcription	Esophagus	oesophagus
40	chr19:36202600-36206200	Weak transcription	A549	lung
41	chr19:36202600-36206400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:36202600-36206600	Weak transcription	NHEK	skin
43	chr19:36203000-36203200	Enhancers	Small Intestine	intestine
44	chr19:36203000-36203800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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