Variant report

Variant	rs4808970
Chromosome Location	chr19:19651140-19651141
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	CREB1	chr19:19650975-19651663	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr19:19650840-19651531	K562	blood:	n/a	n/a
3	MAX	chr19:19650788-19652305	ECC-1	luminal epithelium:	n/a	n/a
4	EGR1	chr19:19651050-19652598	HCT-116	colon:	n/a	chr19:19652507-19652517 chr19:19652255-19652266 chr19:19651676-19651691 chr19:19652257-19652267 chr19:19652254-19652267 chr19:19651678-19651689 chr19:19652207-19652220 chr19:19652257-19652266 chr19:19652254-19652267 chr19:19652256-19652266 chr19:19651679-19651689 chr19:19652507-19652520 chr19:19652529-19652540 chr19:19651389-19651403 chr19:19652254-19652267 chr19:19652527-19652542 chr19:19652255-19652269 chr19:19652256-19652266 chr19:19651677-19651690 chr19:19652250-19652272 chr19:19652529-19652539 chr19:19652529-19652539 chr19:19652254-19652268 chr19:19651677-19651690 chr19:19651680-19651689 chr19:19652212-19652222 chr19:19651677-19651691 chr19:19651440-19651454 chr19:19652253-19652268 chr19:19651677-19651690 chr19:19652254-19652267 chr19:19652527-19652541
5	SIN3A	chr19:19651104-19651252	H1-hESC	embryonic stem cell:	n/a	n/a
6	USF1	chr19:19650986-19651523	ECC-1	luminal epithelium:	n/a	n/a
7	E2F6	chr19:19650689-19651436	H1-hESC	embryonic stem cell:	n/a	n/a
8	HMGN3	chr19:19650944-19651268	K562	blood:	n/a	n/a
9	USF1	chr19:19651077-19651499	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr19:19650990-19651298	K562	blood:	n/a	n/a
11	USF1	chr19:19651083-19651335	K562	blood:	n/a	n/a
12	ELF1	chr19:19651063-19651433	K562	blood:	n/a	n/a
13	MYC	chr19:19651060-19651407	K562	blood:	n/a	n/a
14	E2F6	chr19:19650931-19651562	K562	blood:	n/a	n/a
15	EGR1	chr19:19651130-19651840	K562	blood:	n/a	chr19:19651676-19651691 chr19:19651678-19651689 chr19:19651679-19651689 chr19:19651389-19651403 chr19:19651677-19651690 chr19:19651677-19651690 chr19:19651680-19651689 chr19:19651677-19651691 chr19:19651440-19651454 chr19:19651677-19651690
16	MAX	chr19:19651046-19651418	K562	blood:	n/a	n/a
17	E2F6	chr19:19651027-19651393	K562	blood:	n/a	n/a
18	GABPA	chr19:19650943-19651403	K562	blood:	n/a	n/a
19	USF1	chr19:19651068-19651488	ECC-1	luminal epithelium:	n/a	n/a
20	SP1	chr19:19651045-19651654	H1-hESC	embryonic stem cell:	n/a	chr19:19651372-19651383 chr19:19651306-19651317 chr19:19651357-19651368 chr19:19651322-19651333
21	MXI1	chr19:19650999-19651593	IMR90	lung:	n/a	n/a
22	MAX	chr19:19650965-19651405	K562	blood:	n/a	n/a
23	MAX	chr19:19650872-19652461	HCT-116	colon:	n/a	n/a
24	MYC	chr19:19651071-19651392	K562	blood:	n/a	n/a
25	ELF1	chr19:19651122-19651514	K562	blood:	n/a	n/a
26	MYC	chr19:19651026-19651434	K562	blood:	n/a	n/a
27	RUNX3	chr19:19651068-19651331	GM12878	blood:	n/a	n/a
28	CCNT2	chr19:19651060-19651269	K562	blood:	n/a	n/a
29	GTF2F1	chr19:19651105-19651317	H1-hESC	embryonic stem cell:	n/a	n/a
30	USF1	chr19:19651058-19651455	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr19:19651044-19651339	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr19:19650806-19651494	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr19:19651026-19651453	K562	blood:	n/a	n/a
34	PAX5	chr19:19651078-19651294	GM12892	blood:	n/a	n/a
35	MAX	chr19:19650937-19651489	H1-hESC	embryonic stem cell:	n/a	n/a
36	USF2	chr19:19651085-19651299	H1-hESC	embryonic stem cell:	n/a	n/a
37	CREB1	chr19:19651057-19651665	K562	blood:	n/a	n/a
38	E2F6	chr19:19650798-19651425	K562	blood:	n/a	n/a
39	MYC	chr19:19651082-19651326	H1-hESC	embryonic stem cell:	n/a	n/a
40	MYC	chr19:19651021-19651452	K562	blood:	n/a	n/a
41	BHLHE40	chr19:19651107-19651318	K562	blood:	n/a	n/a
42	USF1	chr19:19651078-19651449	K562	blood:	n/a	n/a
43	CBX3	chr19:19650843-19651726	K562	blood:	n/a	n/a
44	CBX3	chr19:19650999-19651343	K562	blood:	n/a	n/a
45	E2F6	chr19:19650799-19651508	H1-hESC	embryonic stem cell:	n/a	n/a
46	TCF7L2	chr19:19651097-19652110	HCT-116	colon:	n/a	n/a
47	MXI1	chr19:19650942-19652854	SK-N-SH	brain:	n/a	chr19:19652356-19652365
48	MXI1	chr19:19651137-19651320	H1-hESC	embryonic stem cell:	n/a	n/a
49	BCLAF1	chr19:19651011-19651282	GM12878	blood:	n/a	n/a
50	MAX	chr19:19650883-19652275	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19650831..19653075-chr19:20010995..20012617,3	K562	blood:
2	chr19:19649974..19652165-chr19:19739340..19740963,2	MCF-7	breast:
3	chr19:19650697..19653588-chr19:19753029..19754860,3	K562	blood:
4	chr19:19625369..19628375-chr19:19648780..19652325,4	MCF-7	breast:
5	chr19:19649331..19652417-chr19:19771491..19776120,6	K562	blood:
6	chr19:19649879..19653588-chr19:19753029..19755939,4	K562	blood:
7	chr19:19649600..19655493-chr19:19770960..19774805,7	K562	blood:

Variant related genes	Relation type
CILP2	TF binding region
ENSG00000105726	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000267268	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000184635	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000258674	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1036215	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10406278	0.83[EUR][1000 genomes]
rs11085264	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11668203	0.88[EUR][1000 genomes]
rs11669558	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11669730	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670687	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11670761	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670775	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670882	0.94[EUR][1000 genomes]
rs11671253	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1560687	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16996127	0.98[EUR][1000 genomes]
rs17684164	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2060274	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2060275	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2916070	0.84[EUR][1000 genomes]
rs2916072	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2916075	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965179	0.84[EUR][1000 genomes]
rs2965181	0.84[EUR][1000 genomes]
rs2965184	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34487417	0.82[EUR][1000 genomes]
rs34667451	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45556231	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45631651	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808204	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4808205	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808206	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808951	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4808958	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4808962	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808968	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808969	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55927782	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56280531	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56291054	0.82[EUR][1000 genomes]
rs56330647	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58074958	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61744761	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7245689	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7250233	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7252453	0.95[EUR][1000 genomes]
rs7256028	0.98[EUR][1000 genomes]
rs751857	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs754256	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8100927	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8101219	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8102502	0.93[EUR][1000 genomes]
rs8105642	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8110171	0.87[EUR][1000 genomes]
rs8110250	0.86[AMR][1000 genomes];0.88[EUR][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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv911307	chr19:19631655-19657143	Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv911308	chr19:19631655-19663850	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	nsv543928	chr19:19649839-19664043	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4808970	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19630600-19651800	Weak transcription	A549	lung
2	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:19648200-19651400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr19:19648200-19651600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr19:19648400-19651400	Bivalent Enhancer	Fetal Stomach	stomach
6	chr19:19649200-19651400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:19649600-19651400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr19:19649600-19651400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:19649600-19651400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
10	chr19:19649600-19651400	Weak transcription	GM12878-XiMat	blood
11	chr19:19649800-19651400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr19:19649800-19651400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr19:19649800-19651400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr19:19649800-19651400	Weak transcription	Brain Angular Gyrus	brain
15	chr19:19649800-19651600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:19649800-19651600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:19650000-19651400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:19650000-19651400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:19650000-19651400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr19:19650000-19651600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr19:19650000-19651600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:19650200-19651600	Bivalent Enhancer	Primary B cells from cord blood	blood
23	chr19:19650400-19651200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
24	chr19:19650400-19651400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:19650400-19651400	ZNF genes & repeats	Lung	lung
26	chr19:19650400-19651600	ZNF genes & repeats	Spleen	Spleen
27	chr19:19650400-19653000	Bivalent Enhancer	Placenta	Placenta
28	chr19:19650600-19651200	Enhancers	Ovary	ovary
29	chr19:19650600-19651600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr19:19650600-19652600	Enhancers	Gastric	stomach
31	chr19:19650800-19651200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:19650800-19651200	Enhancers	Right Atrium	heart
33	chr19:19650800-19651200	Bivalent/Poised TSS	Thymus	Thymus
34	chr19:19650800-19651400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr19:19650800-19651400	Enhancers	Primary hematopoietic stem cells	blood
36	chr19:19650800-19651400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr19:19650800-19651400	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr19:19650800-19651400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr19:19650800-19651600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:19650800-19651600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
41	chr19:19650800-19651600	Bivalent Enhancer	Fetal Brain Male	brain
42	chr19:19650800-19651600	Bivalent/Poised TSS	Fetal Brain Female	brain
43	chr19:19650800-19651800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr19:19650800-19652200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
45	chr19:19650800-19652200	Bivalent Enhancer	Fetal Lung	lung
46	chr19:19650800-19652400	Enhancers	Pancreas	Pancrea
47	chr19:19650800-19652600	Bivalent Enhancer	Fetal Intestine Small	intestine
48	chr19:19650800-19652800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:19650800-19652800	Enhancers	Fetal Heart	heart
50	chr19:19651000-19651200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood

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