Variant report

Variant	rs1054930
Chromosome Location	chr19:19648346-19648347
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:19648335-19648385	Caco-2	colon:	n/a
2	chr19:19648335-19648385	PANC-1	pancreas:	n/a
3	chr19:19648335-19648385	PFSK-1	brain:	n/a
4	chr19:19648335-19648385	HAEpiC	amniotic membrane:	n/a
5	chr19:19648335-19648385	HEEpiC	esophagus:	n/a
6	chr19:19648335-19648385	AoSMC	blood vessel:	n/a
7	chr19:19648335-19648385	NHBE	bronchial:	n/a
8	chr19:19648335-19648385	AG04449	skin:	fetal
9	chr19:19648335-19648385	HRPEpiC	eye:	n/a
10	chr19:19648335-19648385	LNCaP	prostate:	n/a
11	chr19:19648335-19648385	SK-N-SH_RA	brain:	n/a
12	chr19:19648335-19648385	HIPEpiC	eye:	n/a
13	chr19:19648335-19648385	ProgFib	skin:	n/a
14	chr19:19648335-19648385	GM19239	blood:	n/a
15	chr19:19648335-19648385	GM12892	blood:	n/a
16	chr19:19648335-19648385	HUVEC	blood vessel:	n/a
17	chr19:19648335-19648385	HCM	heart:	n/a
18	chr19:19648335-19648385	A549	lung:	n/a
19	chr19:19648335-19648385	CMK	blood:	n/a
20	chr19:19648335-19648385	NHDF-neo	bronchial:	n/a
21	chr19:19648335-19648385	HRE	kidney:	n/a
22	chr19:19648335-19648385	AG04450	lung:	fetal
23	chr19:19648335-19648385	MCF10A-Er-Src	breast:	n/a
24	chr19:19648335-19648385	AG10803	skin:	n/a
25	chr19:19648335-19648385	T-47D	breast:	n/a
26	chr19:19648335-19648385	BE2_C	brain:	n/a
27	chr19:19648335-19648385	K562	blood:	n/a
28	chr19:19648335-19648385	NT2-D1	testis:	n/a
29	chr19:19648335-19648385	SK-N-SH	brain:	n/a
30	chr19:19648335-19648385	HCF	heart:	n/a
31	chr19:19648335-19648385	MCF-7	breast:	n/a
32	chr19:19648335-19648385	U87	brain:	n/a
33	chr19:19648335-19648385	NB4	blood:	n/a
34	chr19:19648335-19648385	HRCEpiC	kidney:	n/a
35	chr19:19648335-19648385	Hepatocyte	liver:	n/a
36	chr19:19648335-19648385	AG09309	skin:	n/a
37	chr19:19648335-19648385	HCT-116	colon:	n/a
38	chr19:19648335-19648385	HMEC	breast:	n/a
39	chr19:19648335-19648385	BJ	skin:	n/a
40	chr19:19648335-19648385	ovcar-3	ovarian:	n/a
41	chr19:19648335-19648385	AG09319	gingival:	n/a
42	chr19:19648335-19648385	PrEC	prostate:	n/a
43	chr19:19648335-19648385	H1-hESC	embryonic stem cell:	embryo
44	chr19:19648335-19648385	SKMC	muscle:	n/a
45	chr19:19648335-19648385	IMR90	lung:	fetal
46	chr19:19648335-19648385	NH-A	brain:	n/a
47	chr19:19648335-19648385	SK-N-MC	brain:	n/a
48	chr19:19648335-19648385	ECC-1	luminal epithelium:	n/a
49	chr19:19648335-19648385	GM12891	blood:	n/a
50	chr19:19648335-19648385	HEK293	kidney:	embryo

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

No.	Distal block	Cell Line	Cell type
1	chr19:19647870..19650487-chr19:19773815..19776020,2	MCF-7	breast:
2	chr19:19647280..19649688-chr19:19752870..19754432,2	MCF-7	breast:
3	chr19:19625665..19627306-chr19:19648287..19650892,2	K562	blood:
4	chr19:19641380..19649124-chr19:19737025..19742358,12	MCF-7	breast:

No data

Variant related genes	Relation type
CILP2	CpG island
ENSG00000064547	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000105726	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1000237	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10282	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10401193	0.86[ASN][1000 genomes]
rs10402308	0.95[ASN][1000 genomes]
rs10402451	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10402627	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10404728	0.86[ASN][1000 genomes]
rs10405625	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10410664	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10414830	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10419912	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10422819	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047361	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1054284	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1063966	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11669516	0.81[ASN][1000 genomes]
rs12972397	0.81[ASN][1000 genomes]
rs12975119	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12977524	0.81[ASN][1000 genomes]
rs12981405	0.86[ASN][1000 genomes]
rs1465695	0.86[ASN][1000 genomes]
rs1469712	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469713	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1808653	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1858999	0.84[ASN][1000 genomes]
rs1865034	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2082421	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2099333	0.86[ASN][1000 genomes]
rs2099334	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2163804	0.81[ASN][1000 genomes]
rs2163805	0.81[ASN][1000 genomes]
rs2288852	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304098	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2315279	0.82[ASN][1000 genomes]
rs2315281	0.81[ASN][1000 genomes]
rs2315610	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2905431	0.83[ASN][1000 genomes]
rs2916069	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2916073	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2916074	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2916076	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965180	0.84[ASN][1000 genomes]
rs2965182	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2965183	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965188	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2965189	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34277109	0.84[ASN][1000 genomes]
rs34647936	0.81[ASN][1000 genomes]
rs35418933	0.82[ASN][1000 genomes]
rs3752151	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794990	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3794993	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808198	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808199	0.81[ASN][1000 genomes]
rs4808200	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808202	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808203	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808208	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808955	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808957	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808959	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808960	0.81[ASN][1000 genomes]
rs4808961	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4808964	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808965	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808967	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60003758	0.81[ASN][1000 genomes]
rs6511036	0.83[ASN][1000 genomes]
rs6511038	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6909	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7245983	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250893	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252888	0.89[ASN][1000 genomes]
rs7253807	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7256149	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs747050	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs751856	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs751858	0.94[ASN][1000 genomes]
rs754255	0.81[ASN][1000 genomes]
rs892021	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs892022	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9917108	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][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

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19630600-19651800	Weak transcription	A549	lung
2	chr19:19635200-19649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:19638400-19648800	Weak transcription	GM12878-XiMat	blood
4	chr19:19639000-19648600	Weak transcription	Aorta	Aorta
5	chr19:19639600-19648600	Weak transcription	NHLF	lung
6	chr19:19642200-19650600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:19642400-19648600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:19643400-19648400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:19643400-19648800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:19643600-19648400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:19643600-19648600	Weak transcription	Primary T cells from cord blood	blood
12	chr19:19643600-19648600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:19643600-19648600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:19643600-19648600	Weak transcription	Brain Anterior Caudate	brain
15	chr19:19643600-19648600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr19:19643600-19648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:19643600-19648800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:19643800-19648400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:19643800-19648600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:19643800-19648800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:19643800-19648800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr19:19643800-19648800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr19:19643800-19648800	Weak transcription	Right Atrium	heart
25	chr19:19643800-19649000	Weak transcription	Left Ventricle	heart
26	chr19:19644000-19648600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr19:19644000-19648600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:19644200-19649000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:19644200-19649000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:19645400-19648800	Weak transcription	Fetal Heart	heart
31	chr19:19645600-19648800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:19645600-19648800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:19646600-19649600	Weak transcription	Brain Angular Gyrus	brain
34	chr19:19646800-19649000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:19647000-19648600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:19647000-19648800	Weak transcription	Right Ventricle	heart
37	chr19:19647200-19648800	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:19647800-19650000	Enhancers	Spleen	Spleen
39	chr19:19648000-19648400	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr19:19648000-19648400	Enhancers	Duodenum Mucosa	Duodenum
41	chr19:19648000-19648400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
42	chr19:19648000-19648600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:19648000-19648600	Enhancers	NHDF-Ad	bronchial
44	chr19:19648000-19648800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:19648000-19648800	Active TSS	Ovary	ovary
46	chr19:19648000-19649800	Bivalent Enhancer	Fetal Intestine Large	intestine
47	chr19:19648000-19649800	Enhancers	Pancreas	Pancrea
48	chr19:19648200-19648400	Enhancers	Primary T cells fromperipheralblood	blood
49	chr19:19648200-19648400	Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr19:19648200-19648400	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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