Variant report

Variant	rs4808968
Chromosome Location	chr19:19644402-19644403
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	ZNF263	chr19:19643772-19644517	K562	blood:	n/a	chr19:19644297-19644318 chr19:19644249-19644270
2	POLR2A	chr19:19644043-19644421	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZNF263	chr19:19642977-19645281	HEK293-T-REx	kidney:	n/a	chr19:19644297-19644318 chr19:19644249-19644270

No.	Distal block	Cell Line	Cell type
1	chr19:19624801..19628442-chr19:19640614..19645032,4	MCF-7	breast:
2	chr19:19642455..19644774-chr19:19648447..19650007,2	MCF-7	breast:
3	chr19:19644132..19648148-chr19:19648947..19654743,9	K562	blood:
4	chr19:19643099..19644624-chr19:19737632..19740411,2	MCF-7	breast:
5	chr19:19643088..19644986-chr19:19645378..19647778,2	MCF-7	breast:
6	chr19:19640161..19645536-chr19:19752406..19756434,6	K562	blood:
7	chr19:19641380..19649124-chr19:19737025..19742358,12	MCF-7	breast:

Variant related genes	Relation type
CILP2	TF binding region
ENSG00000186010	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000160161	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10406278	0.82[EUR][1000 genomes]
rs11085264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11668203	0.89[EUR][1000 genomes]
rs11669558	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11669730	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670687	0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670882	0.94[CEU][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs11671253	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1560687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17684164	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2060274	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905434	0.81[EUR][1000 genomes]
rs2916070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2916072	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2916075	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965179	0.85[EUR][1000 genomes]
rs2965181	0.85[EUR][1000 genomes]
rs2965184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs2965190	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs2965195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2965201	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs34487417	0.83[EUR][1000 genomes]
rs34667451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45556231	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45631651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808204	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808205	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808206	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808951	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808958	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808970	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55927782	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56280531	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56291054	0.83[EUR][1000 genomes]
rs56330647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58074958	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61744761	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7245689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7250233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7252453	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs7256028	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs751857	1.00[ASW][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs8100927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8101219	0.91[ASW][hapmap];0.96[GIH][hapmap];0.97[LWK][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8102502	0.94[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs8105642	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8111093	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4808968	OCEL1	cis	parietal	SCAN
rs4808968	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs4808968	IL12RB1	cis	parietal	SCAN
rs4808968	GATAD2A	cis	parietal	SCAN
rs4808968	JUND	cis	parietal	SCAN
rs4808968	LSM4	cis	cerebellum	SCAN
rs4808968	DDX49	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19630600-19651800	Weak transcription	A549	lung
2	chr19:19631000-19647800	Weak transcription	HSMMtube	muscle
3	chr19:19635200-19649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:19638400-19648800	Weak transcription	GM12878-XiMat	blood
5	chr19:19639000-19648600	Weak transcription	Aorta	Aorta
6	chr19:19639200-19648000	Weak transcription	Ovary	ovary
7	chr19:19639400-19644800	Weak transcription	Fetal Intestine Large	intestine
8	chr19:19639400-19648200	Weak transcription	Primary B cells from cord blood	blood
9	chr19:19639600-19648600	Weak transcription	NHLF	lung
10	chr19:19640400-19644800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:19640600-19645200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:19641000-19646200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:19641000-19648200	Weak transcription	Gastric	stomach
14	chr19:19642200-19650600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:19642400-19648600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr19:19643000-19645200	Enhancers	Fetal Thymus	thymus
17	chr19:19643000-19645600	Enhancers	Right Ventricle	heart
18	chr19:19643200-19644800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr19:19643200-19645400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr19:19643200-19646600	Weak transcription	NH-A	brain
21	chr19:19643200-19648200	Weak transcription	Lung	lung
22	chr19:19643400-19645200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:19643400-19648000	Weak transcription	NHDF-Ad	bronchial
24	chr19:19643400-19648400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:19643400-19648800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:19643600-19645400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:19643600-19645600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:19643600-19646000	Weak transcription	Brain Hippocampus Middle	brain
29	chr19:19643600-19646400	Weak transcription	Brain Germinal Matrix	brain
30	chr19:19643600-19647000	Weak transcription	Fetal Muscle Leg	muscle
31	chr19:19643600-19647600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:19643600-19647800	Weak transcription	Fetal Brain Female	brain
33	chr19:19643600-19647800	Weak transcription	Spleen	Spleen
34	chr19:19643600-19648000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr19:19643600-19648000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr19:19643600-19648000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:19643600-19648000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:19643600-19648000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr19:19643600-19648000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:19643600-19648000	Weak transcription	Pancreas	Pancrea
41	chr19:19643600-19648200	Weak transcription	Adipose Nuclei	Adipose
42	chr19:19643600-19648200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:19643600-19648200	Weak transcription	HMEC	breast
44	chr19:19643600-19648400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:19643600-19648600	Weak transcription	Primary T cells from cord blood	blood
46	chr19:19643600-19648600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:19643600-19648600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr19:19643600-19648600	Weak transcription	Brain Anterior Caudate	brain
49	chr19:19643600-19648600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr19:19643600-19648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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