Variant report

Variant	rs4808206
Chromosome Location	chr19:19645645-19645646
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19645633-19645894	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr19:19644909-19645919	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:19645641-19645810	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:19645601-19646164	K562	blood:	n/a	n/a
5	POLR2A	chr19:19645508-19646007	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:19645610-19645660	ProgFib	skin:	n/a
2	chr19:19645610-19645660	ECC-1	luminal epithelium:	n/a
3	chr19:19645610-19645660	SK-N-SH	brain:	n/a
4	chr19:19645610-19645660	AG04449	skin:	fetal
5	chr19:19645610-19645660	HEEpiC	esophagus:	n/a
6	chr19:19645610-19645660	GM12891	blood:	n/a
7	chr19:19645610-19645660	RPTEC	kidney:	n/a
8	chr19:19645610-19645660	Hepatocyte	liver:	n/a
9	chr19:19645610-19645660	HRCEpiC	kidney:	n/a
10	chr19:19645610-19645660	PFSK-1	brain:	n/a
11	chr19:19645610-19645660	HPAEpiC	pulmonary alveolar:	n/a
12	chr19:19645610-19645660	BJ	skin:	n/a
13	chr19:19645610-19645660	ovcar-3	ovarian:	n/a
14	chr19:19645610-19645660	AG09319	gingival:	n/a
15	chr19:19645610-19645660	MCF-7	breast:	n/a
16	chr19:19645610-19645660	MCF10A-Er-Src	breast:	n/a
17	chr19:19645610-19645660	HRE	kidney:	n/a
18	chr19:19645610-19645660	K562	blood:	n/a
19	chr19:19645610-19645660	HRPEpiC	eye:	n/a
20	chr19:19645610-19645660	NB4	blood:	n/a
21	chr19:19645610-19645660	Caco-2	colon:	n/a
22	chr19:19645610-19645660	HCPEpiC	choroid plexus:	n/a
23	chr19:19645610-19645660	A549	lung:	n/a
24	chr19:19645610-19645660	CMK	blood:	n/a
25	chr19:19645610-19645660	NHBE	bronchial:	n/a
26	chr19:19645610-19645660	AG09309	skin:	n/a
27	chr19:19645610-19645660	GM19239	blood:	n/a
28	chr19:19645610-19645660	AG10803	skin:	n/a
29	chr19:19645610-19645660	IMR90	lung:	fetal
30	chr19:19645610-19645660	SAEC	small airway:	n/a
31	chr19:19645610-19645660	Hela-S3	cervix:	n/a
32	chr19:19645610-19645660	HUVEC	blood vessel:	n/a
33	chr19:19645610-19645660	GM12878	blood:	n/a
34	chr19:19645610-19645660	HNPCEpiC	eye:	n/a
35	chr19:19645610-19645660	HIPEpiC	eye:	n/a
36	chr19:19645610-19645660	GM12892	blood:	n/a
37	chr19:19645610-19645660	NT2-D1	testis:	n/a
38	chr19:19645610-19645660	AoSMC	blood vessel:	n/a
39	chr19:19645610-19645660	GM06990	blood:	n/a
40	chr19:19645610-19645660	SKMC	muscle:	n/a
41	chr19:19645610-19645660	HAEpiC	amniotic membrane:	n/a
42	chr19:19645610-19645660	BE2_C	brain:	n/a
43	chr19:19645610-19645660	HL-60	blood:	n/a
44	chr19:19645610-19645660	H1-hESC	embryonic stem cell:	embryo
45	chr19:19645610-19645660	HMEC	breast:	n/a
46	chr19:19645610-19645660	HCT-116	colon:	n/a
47	chr19:19645610-19645660	T-47D	breast:	n/a
48	chr19:19645610-19645660	SK-N-MC	brain:	n/a
49	chr19:19645610-19645660	HEK293	kidney:	embryo
50	chr19:19645610-19645660	U87	brain:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19644132..19648148-chr19:19648947..19654743,9	K562	blood:
2	chr19:19643088..19644986-chr19:19645378..19647778,2	MCF-7	breast:
3	chr19:19644634..19646654-chr19:19773130..19774815,2	K562	blood:
4	chr19:19641380..19649124-chr19:19737025..19742358,12	MCF-7	breast:

No data

Variant related genes	Relation type
CILP2	TF binding region
CILP2	CpG island
ENSG00000105726	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000064547	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	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11668203	0.89[EUR][1000 genomes]
rs11669558	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11669730	0.91[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670687	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670761	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670775	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670882	0.94[CEU][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs11671253	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1560687	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17684164	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2060274	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905434	0.81[EUR][1000 genomes]
rs2916070	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2916072	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2916075	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965179	0.85[EUR][1000 genomes]
rs2965181	0.85[EUR][1000 genomes]
rs2965184	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965186	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][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	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap]
rs34487417	0.83[EUR][1000 genomes]
rs34667451	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45556231	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45631651	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808204	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808205	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808951	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808958	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808968	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]
rs4808969	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808970	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55927782	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56280531	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56291054	0.83[EUR][1000 genomes]
rs56330647	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58074958	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61744761	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7245689	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7250233	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7252453	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs7256028	0.99[EUR][1000 genomes]
rs751857	0.91[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754256	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap]
rs8100927	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8101219	0.82[ASW][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.95[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];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];0.86[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
rs4808206	DDX49	cis	cerebellum	SCAN
rs4808206	OCEL1	cis	parietal	SCAN
rs4808206	LSM4	cis	cerebellum	SCAN
rs4808206	IL12RB1	cis	parietal	SCAN
rs4808206	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs4808206	GATAD2A	cis	parietal	SCAN
rs4808206	JUND	cis	parietal	SCAN

Chromatin state (count:72 , 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	chr19:19639400-19648200	Weak transcription	Primary B cells from cord blood	blood
8	chr19:19639600-19648600	Weak transcription	NHLF	lung
9	chr19:19641000-19646200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:19641000-19648200	Weak transcription	Gastric	stomach
11	chr19:19642200-19650600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:19642400-19648600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:19643200-19646600	Weak transcription	NH-A	brain
14	chr19:19643200-19648200	Weak transcription	Lung	lung
15	chr19:19643400-19648000	Weak transcription	NHDF-Ad	bronchial
16	chr19:19643400-19648400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr19:19643400-19648800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:19643600-19646000	Weak transcription	Brain Hippocampus Middle	brain
19	chr19:19643600-19646400	Weak transcription	Brain Germinal Matrix	brain
20	chr19:19643600-19647000	Weak transcription	Fetal Muscle Leg	muscle
21	chr19:19643600-19647600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:19643600-19647800	Weak transcription	Fetal Brain Female	brain
23	chr19:19643600-19647800	Weak transcription	Spleen	Spleen
24	chr19:19643600-19648000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:19643600-19648000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr19:19643600-19648000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:19643600-19648000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:19643600-19648000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr19:19643600-19648000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr19:19643600-19648000	Weak transcription	Pancreas	Pancrea
31	chr19:19643600-19648200	Weak transcription	Adipose Nuclei	Adipose
32	chr19:19643600-19648200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:19643600-19648200	Weak transcription	HMEC	breast
34	chr19:19643600-19648400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:19643600-19648600	Weak transcription	Primary T cells from cord blood	blood
36	chr19:19643600-19648600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:19643600-19648600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr19:19643600-19648600	Weak transcription	Brain Anterior Caudate	brain
39	chr19:19643600-19648600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr19:19643600-19648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:19643600-19648800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:19643800-19646000	Weak transcription	Brain Angular Gyrus	brain
44	chr19:19643800-19646000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:19643800-19646000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:19643800-19646200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr19:19643800-19648000	Weak transcription	Colonic Mucosa	Colon
48	chr19:19643800-19648000	Weak transcription	Thymus	Thymus
49	chr19:19643800-19648200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:19643800-19648200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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