Variant report

Variant	rs8110888
Chromosome Location	chr19:40855255-40855256
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	BHLHE40	chr19:40854987-40855395	K562	blood:	n/a	n/a
2	POLR2A	chr19:40853832-40855318	K562	blood:	n/a	n/a
3	USF1	chr19:40853761-40855378	A549	lung:	n/a	chr19:40854419-40854430
4	TCF12	chr19:40853672-40855441	A549	lung:	n/a	n/a
5	FOS	chr19:40854958-40855327	MCF10A-Er-Src	breast:	n/a	n/a
6	JUND	chr19:40854897-40855352	H1-hESC	embryonic stem cell:	n/a	n/a
7	CEBPB	chr19:40854951-40855391	K562	blood:	n/a	n/a
8	MAX	chr19:40853509-40855470	A549	lung:	n/a	n/a
9	CEBPB	chr19:40854983-40855345	H1-hESC	embryonic stem cell:	n/a	n/a
10	RCOR1	chr19:40854986-40855319	K562	blood:	n/a	n/a
11	MAX	chr19:40854169-40855294	A549	lung:	n/a	n/a
12	MAZ	chr19:40853622-40855561	IMR90	lung:	n/a	n/a
13	POLR2A	chr19:40853925-40855585	H1-neurons	neurons:	n/a	n/a
14	CREB1	chr19:40854053-40855389	GM12878	blood:	n/a	chr19:40855171-40855184
15	USF1	chr19:40853788-40855348	A549	lung:	n/a	chr19:40854419-40854430
16	POLR2A	chr19:40855170-40855469	HepG2	liver:	n/a	n/a
17	CREB1	chr19:40854867-40855310	H1-hESC	embryonic stem cell:	n/a	chr19:40855171-40855184
18	CREB1	chr19:40854944-40855399	H1-hESC	embryonic stem cell:	n/a	chr19:40855171-40855184
19	POLR2A	chr19:40854016-40855293	MCF10A-Er-Src	breast:	n/a	n/a
20	EP300	chr19:40855041-40855306	GM12878	blood:	n/a	n/a
21	SIN3AK20	chr19:40853815-40855463	A549	lung:	n/a	n/a
22	MAX	chr19:40854971-40855368	K562	blood:	n/a	n/a
23	POLR2A	chr19:40853965-40855274	PBDE	blood:	n/a	n/a
24	ATF1	chr19:40854854-40855352	K562	blood:	n/a	n/a
25	SIN3AK20	chr19:40853690-40855570	A549	lung:	n/a	n/a
26	GABPA	chr19:40853808-40855304	A549	lung:	n/a	chr19:40854690-40854699 chr19:40854580-40854594 chr19:40854577-40854591 chr19:40854258-40854267 chr19:40854580-40854591 chr19:40854214-40854223 chr19:40854582-40854591
27	JUN	chr19:40853475-40855517	K562	blood:	n/a	chr19:40854527-40854536 chr19:40855172-40855185 chr19:40854259-40854268
28	MAX	chr19:40854016-40855309	ECC-1	luminal epithelium:	n/a	n/a
29	JUND	chr19:40854851-40855363	HepG2	liver:	n/a	n/a
30	JUN	chr19:40854990-40855327	HepG2	liver:	n/a	chr19:40855172-40855185
31	TBL1XR1	chr19:40855180-40855432	K562	blood:	n/a	n/a
32	POLR2A	chr19:40853771-40855497	MCF10A-Er-Src	breast:	n/a	n/a
33	MXI1	chr19:40853836-40855358	IMR90	lung:	n/a	n/a
34	POLR2A	chr19:40853525-40855377	GM12891	blood:	n/a	n/a
35	EP300	chr19:40853784-40855541	A549	lung:	n/a	chr19:40854277-40854286 chr19:40854258-40854267
36	MAX	chr19:40854802-40855425	K562	blood:	n/a	n/a
37	CEBPB	chr19:40854972-40855431	MCF-7	breast:	n/a	n/a
38	BRCA1	chr19:40853876-40855370	Hela-S3	cervix:	n/a	n/a
39	E2F4	chr19:40855016-40855272	MCF10A-Er-Src	breast:	n/a	n/a
40	MYC	chr19:40854239-40855345	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr19:40854109-40855414	HepG2	liver:	n/a	n/a
42	POLR2A	chr19:40853856-40855290	Hela-S3	cervix:	n/a	n/a
43	SMC3	chr19:40855135-40855282	HepG2	liver:	n/a	n/a
44	ATF3	chr19:40854947-40855374	K562	blood:	n/a	chr19:40855174-40855184 chr19:40855170-40855185 chr19:40855174-40855182
45	MYC	chr19:40854083-40855331	K562	blood:	n/a	n/a
46	ATF3	chr19:40853772-40855604	A549	lung:	n/a	chr19:40855174-40855184 chr19:40855170-40855185 chr19:40854243-40854252 chr19:40855174-40855182 chr19:40854520-40854529 chr19:40854319-40854328 chr19:40854692-40854701
47	POLR2A	chr19:40854965-40855486	HepG2	liver:	n/a	n/a
48	CREB1	chr19:40853945-40855526	HepG2	liver:	n/a	chr19:40855171-40855184
49	CREB1	chr19:40854871-40855412	A549	lung:	n/a	chr19:40855171-40855184
50	SIN3A	chr19:40853637-40855406	H1-hESC	embryonic stem cell:	n/a	chr19:40854213-40854226

No.	Distal block	Cell Line	Cell type
1	chr19:40846921..40852460-chr19:40852861..40856555,6	K562	blood:
2	chr19:40855052..40856726-chr19:40865449..40867831,2	MCF-7	breast:
3	chr19:40853951..40856077-chr19:40931313..40932883,2	MCF-7	breast:
4	chr19:40853192..40856646-chr19:40870044..40873206,4	K562	blood:
5	chr19:40853841..40855507-chr19:41105833..41108523,2	K562	blood:
6	chr19:40853028..40855563-chr19:40876148..40878218,2	K562	blood:
7	chr19:40853787..40856715-chr19:40882110..40885015,2	K562	blood:
8	chr19:40852692..40855852-chr19:40948280..40952207,5	K562	blood:
9	chr19:40854917..40856679-chr19:40945662..40948462,2	MCF-7	breast:
10	chr19:40853920..40856703-chr19:40862603..40866302,4	K562	blood:
11	chr19:40846573..40849159-chr19:40852803..40855284,3	K562	blood:
12	chr19:40853029..40856025-chr19:41082472..41085390,2	K562	blood:
13	chr19:40851266..40855955-chr19:40945466..40950850,6	K562	blood:

Variant related genes	Relation type
C19orf47	TF binding region
ENSG00000105223	Chromatin interaction
ENSG00000206925	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000197019	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10402740	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs10414431	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1129156	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs11668242	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11880261	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.85[ASN][1000 genomes]
rs12609706	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304184	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs2304189	0.89[CHB][hapmap]
rs339526	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs3730050	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs3730051	0.80[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs4239504	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs4239506	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4257318	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4277441	0.81[ASN][1000 genomes]
rs4332845	0.81[ASN][1000 genomes]
rs4337402	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4490099	0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs4499338	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4558508	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs4802070	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs4802071	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4802073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802074	0.83[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803320	0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs6508936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7248338	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7249146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250897	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs7255581	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257972	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7260106	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260517	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.86[ASN][1000 genomes]
rs748236	0.84[ASN][1000 genomes]
rs8100018	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8102171	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs8104727	0.81[ASN][1000 genomes]
rs969531	0.87[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs9749283	0.82[EUR][1000 genomes];0.83[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	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv2754051	chr19:40848081-40863842	Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription 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 miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs8110888	C19orf47	cis	multi-tissue	Pritchard
rs8110888	EMP3	cis	cerebellum	SCAN
rs8110888	ERCC1	cis	parietal	SCAN
rs8110888	SYMPK	cis	cerebellum	SCAN
rs8110888	ZNF221	cis	parietal	SCAN
rs8110888	PPP1R13L	cis	cerebellum	SCAN
rs8110888	C19orf47	cis	lymphoblastoid	seeQTL
rs8110888	FLJ36888	cis	multi-tissue	Pritchard
rs8110888	TMEM91	cis	parietal	SCAN
rs8110888	APOE	cis	cerebellum	SCAN
rs8110888	SPACA4	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40852800-40855600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:40852800-40855600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:40853000-40855800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr19:40853200-40855400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:40853400-40855400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr19:40853400-40855600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:40853400-40855600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr19:40853400-40855600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr19:40853600-40855400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr19:40853600-40855400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr19:40853600-40855400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:40853600-40855400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:40853600-40855400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:40853600-40855400	Active TSS	Aorta	Aorta
15	chr19:40853600-40855400	Active TSS	Fetal Brain Female	brain
16	chr19:40853600-40855400	Active TSS	Psoas Muscle	Psoas
17	chr19:40853600-40855600	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr19:40853600-40855600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:40853600-40855600	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr19:40853600-40855600	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr19:40853800-40855400	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr19:40853800-40855400	Active TSS	Placenta Amnion	Placenta Amnion
23	chr19:40853800-40855600	Active TSS	Fetal Intestine Large	intestine
24	chr19:40854600-40855400	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr19:40854600-40855600	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr19:40854800-40855400	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr19:40854800-40855400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:40854800-40855400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr19:40854800-40855400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:40854800-40855400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:40854800-40855400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr19:40854800-40855400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:40854800-40855400	Flanking Active TSS	Fetal Thymus	thymus
34	chr19:40854800-40855600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:40854800-40855600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr19:40854800-40855600	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr19:40854800-40855600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr19:40854800-40855600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr19:40854800-40855600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:40854800-40855600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:40854800-40855600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr19:40854800-40855600	Flanking Active TSS	Liver	Liver
43	chr19:40854800-40855600	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr19:40854800-40855600	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr19:40854800-40855600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr19:40854800-40855600	Flanking Active TSS	Dnd41	blood
47	chr19:40854800-40855600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr19:40855000-40855400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:40855000-40855400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr19:40855000-40855400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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