Variant report

Variant	rs234369
Chromosome Location	chr19:40476737-40476738
allele	A/G
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	CTCF	chr19:40476700-40476850	NHEK	skin:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
2	RAD21	chr19:40476588-40476906	GM12878	blood:	n/a	n/a
3	CTCF	chr19:40476702-40476973	Hela-S3	cervix:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
4	CREB1	chr19:40476461-40477413	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr19:40476589-40477030	HepG2	liver:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
6	MYBL2	chr19:40476443-40477166	HepG2	liver:	n/a	n/a
7	USF2	chr19:40476445-40477065	GM12878	blood:	n/a	chr19:40476888-40476904 chr19:40476900-40476916
8	CTCF	chr19:40476653-40476995	GM19240	blood:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
9	GABPA	chr19:40476699-40477295	H1-hESC	embryonic stem cell:	n/a	chr19:40476873-40476887 chr19:40476876-40476890
10	CTCF	chr19:40476720-40476870	HEEpiC	esophagus:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
11	FOXM1	chr19:40476379-40477319	GM12878	blood:	n/a	n/a
12	CTCF	chr19:40476718-40476945	GM20000	blood:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
13	BRCA1	chr19:40476667-40477239	Hela-S3	cervix:	n/a	n/a
14	TBL1XR1	chr19:40476268-40477275	K562	blood:	n/a	n/a
15	TBP	chr19:40476575-40477283	HepG2	liver:	n/a	n/a
16	EP300	chr19:40476028-40477514	A549	lung:	n/a	chr19:40477350-40477363
17	MAZ	chr19:40476208-40477210	GM12878	blood:	n/a	chr19:40476864-40476871
18	USF1	chr19:40476465-40477284	ECC-1	luminal epithelium:	n/a	chr19:40476888-40476904 chr19:40476900-40476916
19	MAX	chr19:40476303-40477244	K562	blood:	n/a	chr19:40476864-40476871
20	POLR2A	chr19:40476383-40477338	ProgFib	skin:	n/a	n/a
21	CREB1	chr19:40476737-40477306	ECC-1	luminal epithelium:	n/a	n/a
22	THAP1	chr19:40476560-40476971	K562	blood:	n/a	n/a
23	EGR1	chr19:40476708-40476965	GM12878	blood:	n/a	chr19:40476898-40476911
24	GABPA	chr19:40476712-40477261	HepG2	liver:	n/a	chr19:40476873-40476887 chr19:40476876-40476890
25	CTCF	chr19:40476716-40476977	GM13976	blood:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
26	MAX	chr19:40476239-40477231	H1-hESC	embryonic stem cell:	n/a	chr19:40476864-40476871
27	CTCF	chr19:40476633-40477004	GM12891	blood:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
28	RELA	chr19:40476161-40477348	GM15510	blood:	n/a	n/a
29	CTCF	chr19:40476720-40476870	BE2_C	brain:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
30	MAX	chr19:40476220-40477357	HepG2	liver:	n/a	chr19:40476864-40476871
31	MAX	chr19:40476194-40477259	K562	blood:	n/a	chr19:40476864-40476871
32	RAD21	chr19:40476301-40477126	Hela-S3	cervix:	n/a	n/a
33	SIX5	chr19:40476729-40477294	GM12878	blood:	n/a	chr19:40477012-40477021 chr19:40477008-40477022 chr19:40477010-40477019
34	REST	chr19:40476010-40477874	A549	lung:	n/a	chr19:40477231-40477245 chr19:40476921-40476930
35	CTCF	chr19:40476700-40476850	GM12873	blood:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
36	CCNT2	chr19:40476680-40477203	K562	blood:	n/a	chr19:40476831-40476840
37	CEBPB	chr19:40476282-40477243	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr19:40476141-40477442	GM12892	blood:	n/a	n/a
39	HEY1	chr19:40476267-40477410	K562	blood:	n/a	n/a
40	SIX5	chr19:40475915-40477743	A549	lung:	n/a	chr19:40477012-40477021 chr19:40477008-40477022 chr19:40477010-40477019
41	CTCF	chr19:40476647-40476995	NHEK	skin:	n/a	chr19:40476809-40476825 chr19:40476810-40476823 chr19:40476808-40476826
42	YY1	chr19:40476614-40477196	K562	blood:	n/a	chr19:40476806-40476820
43	GABPA	chr19:40476469-40477498	K562	blood:	n/a	chr19:40476873-40476887 chr19:40476876-40476890
44	SIX5	chr19:40476728-40477244	GM12878	blood:	n/a	chr19:40477012-40477021 chr19:40477008-40477022 chr19:40477010-40477019
45	BCL3	chr19:40475837-40478638	A549	lung:	n/a	chr19:40477755-40477762 chr19:40476909-40476922 chr19:40476887-40476895
46	USF1	chr19:40476477-40477153	A549	lung:	n/a	chr19:40476888-40476904 chr19:40476900-40476916
47	POLR2A	chr19:40476540-40477302	H1-hESC	embryonic stem cell:	n/a	n/a
48	POU2F2	chr19:40476563-40476952	GM12878	blood:	n/a	chr19:40476882-40476894
49	RCOR1	chr19:40476443-40477289	Hela-S3	cervix:	n/a	n/a
50	BACH1	chr19:40476429-40477075	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40475224..40479165-chr19:40500138..40503908,5	MCF-7	breast:
2	chr19:40476443..40477007-chr4:109541231..109541965,2	Hela-S3	cervix:
3	chr19:40475779..40479202-chr19:40484390..40487184,3	MCF-7	breast:
4	chr19:40476074..40478265-chr19:40727904..40730547,2	K562	blood:
5	chr19:40476362..40476867-chr8:48650522..48651379,2	Hela-S3	cervix:
6	chr19:40471803..40479510-chr19:40500414..40506141,13	K562	blood:
7	chr19:40476701..40477573-chr2:58468129..58468983,2	Hela-S3	cervix:
8	chr19:40474074..40479560-chr19:40500872..40505885,15	K562	blood:
9	chr19:40475954..40476782-chr9:140094691..140095436,2	Hela-S3	cervix:
10	chr19:40335423..40338376-chr19:40475745..40478585,3	MCF-7	breast:
11	chr19:40473843..40476809-chr19:40580140..40582711,2	K562	blood:
12	chr19:40476601..40478274-chr19:40696597..40698505,2	MCF-7	breast:
13	chr19:40476652..40477565-chr8:134309018..134309549,2	Hela-S3	cervix:
14	chr19:40475223..40478471-chr19:40501440..40504433,4	MCF-7	breast:
15	chr11:8703528..8704467-chr19:40476058..40476859,2	Hela-S3	cervix:
16	chr19:40475627..40477448-chr19:40488528..40491173,2	MCF-7	breast:
17	chr19:40474771..40476909-chr19:40510895..40513738,3	K562	blood:
18	chr19:40471964..40473535-chr19:40475290..40476792,2	K562	blood:
19	chr12:27091241..27091864-chr19:40476355..40476971,2	Hela-S3	cervix:
20	chr19:40475179..40477026-chr19:40560831..40562342,2	K562	blood:
21	chr19:40476351..40476870-chr21:27392238..27393165,2	Hela-S3	cervix:
22	chr19:40473089..40482317-chr19:40483091..40492558,21	K562	blood:
23	chr19:40476398..40477126-chr8:144640195..144640964,2	HCT-116	colon:

Variant related genes	Relation type
PSMC4	TF binding region
ENSG00000104419	Chromatin interaction
ENSG00000013275	Chromatin interaction
ENSG00000115392	Chromatin interaction
ENSG00000234492	Chromatin interaction
ENSG00000105219	Chromatin interaction
ENSG00000130758	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000111790	Chromatin interaction
ENSG00000104518	Chromatin interaction
ENSG00000273063	Chromatin interaction
ENSG00000064102	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000176058	Chromatin interaction
ENSG00000128000	Chromatin interaction
ENSG00000187187	Chromatin interaction
ENSG00000109475	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10421829	1.00[CHB][hapmap]
rs16973959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173062	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234329	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs234335	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234336	1.00[ASN][1000 genomes]
rs234337	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234338	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs234344	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234345	1.00[ASN][1000 genomes]
rs234347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234349	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234351	1.00[ASN][1000 genomes]
rs234362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234364	1.00[ASN][1000 genomes]
rs234366	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234373	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531363	1.00[CHB][hapmap]
rs2542325	1.00[ASN][1000 genomes]
rs2542328	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337796	1.00[CHB][hapmap]
rs376630	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378554	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399405	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs420413	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs512360	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58294889	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616965	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60025633	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61413463	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249398	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255173	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259136	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7260610	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8113194	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913212	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv9726	chr19:40476453-40478048	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40475800-40477200	Active TSS	Primary T cells from cord blood	blood
2	chr19:40475800-40477600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr19:40475800-40477600	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr19:40475800-40477600	Active TSS	NHEK	skin
5	chr19:40476000-40476800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr19:40476000-40476800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:40476000-40476800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr19:40476000-40476800	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr19:40476000-40477400	Active TSS	Brain Germinal Matrix	brain
10	chr19:40476000-40477400	Active TSS	Thymus	Thymus
11	chr19:40476000-40477600	Active TSS	Brain Cingulate Gyrus	brain
12	chr19:40476000-40477600	Active TSS	Fetal Lung	lung
13	chr19:40476000-40477600	Active TSS	Fetal Stomach	stomach
14	chr19:40476000-40477600	Active TSS	Right Ventricle	heart
15	chr19:40476000-40477800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:40476000-40477800	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr19:40476000-40477800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:40476000-40477800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:40476000-40477800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr19:40476000-40477800	Active TSS	Small Intestine	intestine
21	chr19:40476000-40477800	Active TSS	NHDF-Ad	bronchial
22	chr19:40476000-40477800	Active TSS	NHLF	lung
23	chr19:40476000-40478000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:40476000-40478000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:40476000-40478000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:40476000-40478000	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr19:40476000-40478000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr19:40476000-40478000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:40476000-40478000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:40476000-40478000	Active TSS	Psoas Muscle	Psoas
31	chr19:40476000-40478000	Active TSS	HSMM	muscle
32	chr19:40476000-40478200	Active TSS	H9 Cell Line	embryonic stem cell
33	chr19:40476000-40478200	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr19:40476000-40478200	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr19:40476000-40478200	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr19:40476000-40478200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:40476000-40478200	Active TSS	Right Atrium	heart
38	chr19:40476200-40476800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr19:40476200-40476800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr19:40476200-40476800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:40476200-40476800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:40476200-40476800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:40476200-40476800	Flanking Active TSS	Placenta	Placenta
44	chr19:40476200-40477600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:40476200-40477600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:40476200-40477600	Active TSS	Fetal Brain Male	brain
47	chr19:40476200-40477600	Active TSS	Fetal Heart	heart
48	chr19:40476200-40477600	Active TSS	Ovary	ovary
49	chr19:40476200-40477600	Active TSS	Spleen	Spleen
50	chr19:40476200-40477800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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