Variant report

Variant	rs7247178
Chromosome Location	chr19:52815890-52815891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52810214..52812761-chr19:52813239..52815974,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10404965	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10405321	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10407594	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10408636	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10411053	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10415728	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10419765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11084147	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11084148	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11667008	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12462904	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12462953	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12973842	0.81[AMR][1000 genomes]
rs1540745	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs167707	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs167708	0.82[ASN][1000 genomes]
rs170414	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1810006	0.87[ASN][1000 genomes]
rs2115075	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2115076	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2657933	0.88[ASN][1000 genomes]
rs321902	0.84[ASN][1000 genomes]
rs321919	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs321921	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs321922	0.89[ASN][1000 genomes]
rs321923	0.91[ASN][1000 genomes]
rs321924	0.87[ASN][1000 genomes]
rs321925	0.89[ASN][1000 genomes]
rs321926	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs321928	0.81[ASN][1000 genomes]
rs321932	0.81[ASN][1000 genomes]
rs321934	0.81[ASN][1000 genomes]
rs321935	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4801912	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802920	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7249338	0.84[ASN][1000 genomes]
rs7249784	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7256570	0.91[ASN][1000 genomes]
rs7258711	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7260178	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109096	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8109646	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8112051	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8112337	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs8113784	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs890842	0.89[JPT][hapmap]
rs890843	0.86[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	esv3394228	chr19:52810905-52816835	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7247178	ZNF329	cis	cerebellum	SCAN
rs7247178	ZNF480	cis	lymphoblastoid	seeQTL
rs7247178	NAT14	cis	parietal	SCAN
rs7247178	ZNF480	Cis_1M	lymphoblastoid	RTeQTL
rs7247178	ZNF677	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52801800-52827200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:52801800-52829200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:52802000-52826400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:52802000-52830000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:52802200-52827400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr19:52802200-52828400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:52802200-52829200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
8	chr19:52802400-52828800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
9	chr19:52802400-52841800	ZNF genes & repeats	Liver	Liver
10	chr19:52802600-52826800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr19:52802600-52827600	ZNF genes & repeats	Dnd41	blood
12	chr19:52803800-52816200	ZNF genes & repeats	Small Intestine	intestine
13	chr19:52803800-52829000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
14	chr19:52803800-52829200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr19:52804400-52827200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
16	chr19:52805000-52819000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr19:52805200-52829000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
18	chr19:52805400-52829200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:52805600-52827800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:52807400-52824400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
21	chr19:52807400-52824800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:52807800-52816200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
23	chr19:52807800-52827000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr19:52808000-52824200	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr19:52808200-52826200	ZNF genes & repeats	Thymus	Thymus
26	chr19:52808200-52827200	ZNF genes & repeats	Left Ventricle	heart
27	chr19:52808200-52831800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
28	chr19:52808400-52817600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:52808400-52826200	ZNF genes & repeats	Placenta	Placenta
30	chr19:52808400-52826600	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr19:52808400-52827200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:52808600-52816000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:52808600-52824400	ZNF genes & repeats	Fetal Stomach	stomach
34	chr19:52808600-52828000	ZNF genes & repeats	Fetal Lung	lung
35	chr19:52809000-52816000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
36	chr19:52809200-52829800	ZNF genes & repeats	Primary T cells from cord blood	blood
37	chr19:52810600-52826400	ZNF genes & repeats	Fetal Intestine Large	intestine
38	chr19:52811000-52826400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
39	chr19:52811200-52818000	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr19:52812600-52816200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:52813000-52817000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:52813000-52817400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr19:52813000-52817400	Weak transcription	Brain Angular Gyrus	brain
44	chr19:52813000-52817400	Weak transcription	Brain Substantia Nigra	brain
45	chr19:52813000-52817400	Weak transcription	HSMMtube	muscle
46	chr19:52813000-52818200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:52813000-52818800	Weak transcription	Brain Anterior Caudate	brain
48	chr19:52813000-52818800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:52813000-52819000	Weak transcription	Osteobl	bone
50	chr19:52813000-52819600	Weak transcription	HUVEC	blood vessel

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