Variant report

Variant	rs321935
Chromosome Location	chr19:52828640-52828641
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52827319..52831915-chr19:52837582..52840953,5	MCF-7	breast:
2	chr19:52828291..52831274-chr19:52840252..52843029,2	K562	blood:
3	chr19:52822040..52824431-chr19:52826518..52828994,2	K562	blood:
4	chr19:52823009..52826195-chr19:52826633..52829397,3	K562	blood:

Variant related genes	Relation type
ENSG00000167554	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10404965	0.86[ASN][1000 genomes]
rs10405321	0.86[ASN][1000 genomes]
rs10407594	0.88[ASN][1000 genomes]
rs10408636	0.88[ASN][1000 genomes]
rs10411053	0.86[ASN][1000 genomes]
rs10415728	0.88[ASN][1000 genomes]
rs10419765	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs11084148	0.86[ASN][1000 genomes]
rs12462953	0.84[JPT][hapmap]
rs1540745	0.84[ASN][1000 genomes]
rs167707	0.82[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs167708	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs170414	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1810006	0.85[ASN][1000 genomes]
rs2115075	0.96[ASN][1000 genomes]
rs2115076	0.86[ASN][1000 genomes]
rs2657933	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs321902	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs321912	0.93[CEU][hapmap]
rs321919	0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs321921	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs321922	0.86[ASN][1000 genomes]
rs321923	0.88[ASN][1000 genomes]
rs321924	0.85[ASN][1000 genomes]
rs321925	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs321926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs321928	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321932	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321934	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4801912	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7247178	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7249338	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7249784	0.88[ASN][1000 genomes]
rs7254876	0.81[ASN][1000 genomes]
rs7256570	0.88[ASN][1000 genomes]
rs7260178	0.82[ASN][1000 genomes]
rs8102373	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs890842	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv912299	chr19:52795985-52832830	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
10	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
11	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs321935	ZBTB45	cis	cerebellum	SCAN
rs321935	TCF7L2	trans	parietal	SCAN
rs321935	ZFP28	cis	parietal	SCAN
rs321935	VN1R4	cis	parietal	SCAN
rs321935	ZNF665	cis	parietal	SCAN
rs321935	ZNF470	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52801800-52829200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52802000-52830000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:52802200-52829200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr19:52802400-52828800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
5	chr19:52802400-52841800	ZNF genes & repeats	Liver	Liver
6	chr19:52803800-52829000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
7	chr19:52803800-52829200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
8	chr19:52805200-52829000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
9	chr19:52805400-52829200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:52808200-52831800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr19:52809200-52829800	ZNF genes & repeats	Primary T cells from cord blood	blood
12	chr19:52814600-52829400	ZNF genes & repeats	Colon Smooth Muscle	Colon
13	chr19:52814600-52836600	ZNF genes & repeats	Adipose Nuclei	Adipose
14	chr19:52814800-52828800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:52814800-52829200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
16	chr19:52814800-52830000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:52814800-52831400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr19:52814800-52831400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr19:52815000-52829200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:52816800-52829200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:52817200-52830200	ZNF genes & repeats	Fetal Brain Female	brain
22	chr19:52817400-52828800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:52817400-52829000	ZNF genes & repeats	Psoas Muscle	Psoas
24	chr19:52818200-52829200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
25	chr19:52818400-52829200	ZNF genes & repeats	Brain Germinal Matrix	brain
26	chr19:52818800-52829200	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
27	chr19:52819800-52829000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:52821800-52829400	ZNF genes & repeats	Brain Hippocampus Middle	brain
29	chr19:52826200-52829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:52826800-52828800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:52827200-52829000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:52827200-52829000	Weak transcription	Placenta	Placenta
33	chr19:52827200-52829200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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