Variant report

Variant	rs8111400
Chromosome Location	chr19:38422754-38422755
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	ZBTB33	chr19:38422506-38423382	A549	lung:	n/a	n/a
2	POLR2A	chr19:38422384-38423482	GM12892	blood:	n/a	n/a
3	TBP	chr19:38422446-38423165	GM12878	blood:	n/a	n/a
4	STAT3	chr19:38422413-38422774	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:38422673-38422903	HepG2	liver:	n/a	n/a
6	CTCF	chr19:38422620-38422770	HA-sp	spinal cord:	n/a	n/a
7	ATF3	chr19:38422396-38424733	A549	lung:	n/a	n/a
8	POLR2A	chr19:38422517-38423334	A549	lung:	n/a	n/a
9	CTCF	chr19:38422640-38422790	AG09319	gingival:	n/a	n/a
10	SP1	chr19:38422277-38425218	A549	lung:	n/a	n/a
11	RELA	chr19:38422564-38423321	GM19099	blood:	n/a	n/a
12	USF1	chr19:38422692-38423408	ECC-1	luminal epithelium:	n/a	chr19:38422964-38422975
13	CTCF	chr19:38422740-38422890	HPF	lung:	n/a	n/a
14	CTCF	chr19:38422660-38422810	HRPEpiC	eye:	n/a	n/a
15	CTCF	chr19:38422665-38422862	GM12892	blood:	n/a	n/a
16	CTCF	chr19:38422749-38422809	Fibrobl	skin:	n/a	n/a
17	CEBPB	chr19:38422706-38422884	HepG2	liver:	n/a	n/a
18	JUND	chr19:38422420-38423404	A549	lung:	n/a	n/a
19	USF1	chr19:38422530-38423210	A549	lung:	n/a	chr19:38422964-38422975
20	CTCF	chr19:38422693-38422861	MCF-7	breast:	n/a	n/a
21	CTCF	chr19:38422660-38422810	AG10803	skin:	n/a	n/a
22	TEAD4	chr19:38422734-38423397	H1-hESC	embryonic stem cell:	n/a	n/a
23	RAD21	chr19:38422571-38423219	HepG2	liver:	n/a	chr19:38422831-38422841
24	CTCF	chr19:38422667-38422790	Pancreas_OC	pancreas:	n/a	n/a
25	POLR2A	chr19:38422573-38423386	HL-60	blood:	n/a	n/a
26	FOXA2	chr19:38422444-38424138	A549	lung:	n/a	n/a
27	CTCF	chr19:38422620-38422770	HVMF	connective:	n/a	n/a
28	POLR2A	chr19:38422536-38423169	HepG2	liver:	n/a	n/a
29	RUNX3	chr19:38422442-38423364	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:38422694-38423439	MCF-7	breast:	n/a	n/a
31	CTCF	chr19:38422708-38422813	GM10248	blood:	n/a	n/a
32	ELF1	chr19:38422418-38423669	A549	lung:	n/a	n/a
33	POLR2A	chr19:38422627-38423345	HepG2	liver:	n/a	n/a
34	MAX	chr19:38422640-38423417	H1-hESC	embryonic stem cell:	n/a	chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422965-38422974 chr19:38422963-38422976 chr19:38422964-38422973 chr19:38422963-38422976 chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422964-38422975
35	MBD4	chr19:38422365-38422890	HepG2	liver:	n/a	n/a
36	TAF1	chr19:38422600-38423271	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr19:38422640-38422790	GM12865	blood:	n/a	n/a
38	POLR2A	chr19:38422467-38423254	HepG2	liver:	n/a	n/a
39	CTCF	chr19:38422720-38422870	HMEC	breast:	n/a	n/a
40	CTCF	chr19:38422660-38422810	HCPEpiC	choroid plexus:	n/a	n/a
41	MXI1	chr19:38422696-38423241	H1-hESC	embryonic stem cell:	n/a	chr19:38422964-38422973 chr19:38422966-38422975
42	POLR2A	chr19:38422594-38423280	GM12891	blood:	n/a	n/a
43	MAX	chr19:38422503-38423390	NB4	blood:	n/a	chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422965-38422974 chr19:38422963-38422976 chr19:38422964-38422973 chr19:38422963-38422976 chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422964-38422975
44	POLR2A	chr19:38422509-38423395	ECC-1	luminal epithelium:	n/a	n/a
45	WRNIP1	chr19:38422420-38423637	GM12878	blood:	n/a	n/a
46	CTCF	chr19:38422700-38422850	AG09319	gingival:	n/a	n/a
47	CTCF	chr19:38422692-38422855	MCF-7	breast:	n/a	n/a
48	SIN3AK20	chr19:38422399-38423661	A549	lung:	n/a	n/a
49	CTCF	chr19:38422680-38422830	HPF	lung:	n/a	n/a
50	TEAD4	chr19:38422624-38423497	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:
3	chr19:38420982..38422890-chr19:38471015..38472804,2	MCF-7	breast:

Variant related genes	Relation type
SIPA1L3	TF binding region
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10422056	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083438	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11083439	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11668384	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11668558	1.00[CHB][hapmap]
rs12462485	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12610891	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1632177	0.82[EUR][1000 genomes]
rs1643464	0.81[EUR][1000 genomes]
rs1643465	0.81[EUR][1000 genomes]
rs1643470	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1643472	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1725468	0.81[EUR][1000 genomes]
rs1725490	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17306795	0.91[CHB][hapmap]
rs241937	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs241940	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs241941	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs241942	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs241943	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs241944	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs241946	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs241947	0.83[ASN][1000 genomes]
rs241948	1.00[CHB][hapmap]
rs241951	0.90[CHB][hapmap]
rs241957	0.83[ASN][1000 genomes]
rs241959	0.87[ASN][1000 genomes]
rs241960	0.87[ASN][1000 genomes]
rs353405	0.92[EUR][1000 genomes]
rs353406	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs353409	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs353412	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs353413	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3752365	1.00[CHB][hapmap]
rs3894129	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4482404	1.00[CHB][hapmap]
rs4802134	1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803536	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803566	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108355	0.82[AMR][1000 genomes]
rs6508748	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6508752	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs697433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250668	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7254828	1.00[CHB][hapmap]
rs7255551	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8102871	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8103882	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8105694	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8110417	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833915	0.81[EUR][1000 genomes]
rs833916	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs856302	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs856309	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs861308	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases
3	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
5	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:38405600-38422800	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:38412000-38423800	Weak transcription	Lung	lung
9	chr19:38412200-38422800	Weak transcription	Adipose Nuclei	Adipose
10	chr19:38412200-38423000	Weak transcription	Thymus	Thymus
11	chr19:38418800-38425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:38419400-38424800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:38419800-38422800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr19:38419800-38422800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:38420200-38425000	Weak transcription	Small Intestine	intestine
16	chr19:38421000-38423200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr19:38421200-38424400	Enhancers	Fetal Heart	heart
18	chr19:38421200-38425000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:38421600-38422800	Weak transcription	Gastric	stomach
20	chr19:38421600-38424800	Enhancers	Fetal Thymus	thymus
21	chr19:38421800-38422800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:38421800-38423800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr19:38421800-38425400	Enhancers	Fetal Muscle Trunk	muscle
24	chr19:38421800-38425400	Enhancers	Fetal Muscle Leg	muscle
25	chr19:38422000-38422800	Enhancers	Fetal Stomach	stomach
26	chr19:38422000-38422800	Weak transcription	Pancreas	Pancrea
27	chr19:38422000-38422800	Enhancers	HSMMtube	muscle
28	chr19:38422000-38426400	Weak transcription	Primary T cells from cord blood	blood
29	chr19:38422200-38422800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr19:38422200-38422800	Weak transcription	Stomach Mucosa	stomach
31	chr19:38422200-38423400	Active TSS	A549	lung
32	chr19:38422200-38425000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:38422200-38425600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:38422400-38422800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr19:38422400-38422800	Enhancers	Brain Substantia Nigra	brain
36	chr19:38422400-38422800	Enhancers	Colonic Mucosa	Colon
37	chr19:38422400-38422800	Enhancers	NHLF	lung
38	chr19:38422400-38423000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr19:38422400-38423000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:38422400-38423000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr19:38422400-38423000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr19:38422400-38423200	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr19:38422400-38423200	Active TSS	Stomach Smooth Muscle	stomach
44	chr19:38422400-38423200	Active TSS	HepG2	liver
45	chr19:38422400-38423600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr19:38422400-38423600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr19:38422400-38423600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr19:38422400-38423600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr19:38422400-38423600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:38422400-38423600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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