Variant report

Variant	rs3885340
Chromosome Location	chr19:38807490-38807491
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38806017-38808215	K562	blood:	n/a	n/a
2	ARID3A	chr19:38807469-38808195	K562	blood:	n/a	n/a
3	RCOR1	chr19:38806029-38808321	K562	blood:	n/a	n/a
4	CBX3	chr19:38807381-38808184	K562	blood:	n/a	n/a
5	TBL1XR1	chr19:38805898-38808243	K562	blood:	n/a	n/a
6	JUND	chr19:38806043-38808215	K562	blood:	n/a	n/a
7	JUN	chr19:38805648-38808373	K562	blood:	n/a	n/a
8	CBX3	chr19:38807385-38808233	K562	blood:	n/a	n/a
9	POLR2A	chr19:38805864-38808241	K562	blood:	n/a	n/a
10	TCF12	chr19:38805799-38807504	A549	lung:	n/a	n/a
11	GATA1	chr19:38806737-38808245	PBDE	blood:	n/a	chr19:38807885-38807902
12	POLR2A	chr19:38805908-38808270	K562	blood:	n/a	n/a
13	SIX5	chr19:38806642-38807551	A549	lung:	n/a	chr19:38807166-38807180
14	EP300	chr19:38805951-38808272	K562	blood:	n/a	chr19:38807244-38807258
15	POLR2A	chr19:38805955-38808225	K562	blood:	n/a	n/a
16	GATA1	chr19:38805822-38808311	K562	blood:	n/a	chr19:38806077-38806087 chr19:38807885-38807902
17	GATA2	chr19:38806931-38807572	SH-SY5Y	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38804679..38808674-chr19:38824887..38827856,7	K562	blood:
2	chr19:38805296..38807779-chr19:38877097..38880049,2	K562	blood:
3	chr19:38806332..38809400-chr19:38825014..38828541,5	K562	blood:
4	chr19:38800007..38802686-chr19:38805252..38808238,5	K562	blood:
5	chr19:38746183..38748575-chr19:38806704..38809483,2	K562	blood:
6	chr19:38805271..38808237-chr19:39322535..39325453,2	K562	blood:
7	chr19:38795298..38801659-chr19:38801673..38807893,10	K562	blood:
8	chr19:38806279..38807928-chr19:38863720..38866328,2	K562	blood:
9	chr19:38745470..38748025-chr19:38806544..38809528,4	K562	blood:

No data

Variant related genes	Relation type
YIF1B	TF binding region
KCNK6	TF binding region
ENSG00000099341	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000167641	Chromatin interaction
ENSG00000188766	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs61734615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73037321	1.00[EUR][1000 genomes]
rs73037333	0.97[EUR][1000 genomes]
rs73037343	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73037346	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73041292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043012	0.87[EUR][1000 genomes]
rs73043013	0.87[EUR][1000 genomes]
rs73043014	0.87[EUR][1000 genomes]
rs73043015	0.87[EUR][1000 genomes]
rs73043019	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73043021	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73043022	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73043027	0.87[EUR][1000 genomes]
rs73043028	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73043029	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73043030	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73043033	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73043098	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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv960928	chr19:38790012-38822380	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38806200-38807800	Active TSS	Brain Anterior Caudate	brain
2	chr19:38806200-38807800	Active TSS	Brain Cingulate Gyrus	brain
3	chr19:38806200-38808000	Active TSS	Brain Hippocampus Middle	brain
4	chr19:38806400-38807800	Active TSS	Colonic Mucosa	Colon
5	chr19:38806400-38807800	Active TSS	Duodenum Mucosa	Duodenum
6	chr19:38806400-38808000	Active TSS	Rectal Smooth Muscle	rectum
7	chr19:38806400-38810200	Enhancers	Fetal Heart	heart
8	chr19:38806600-38809200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:38806800-38807800	Active TSS	Right Atrium	heart
10	chr19:38806800-38808000	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr19:38806800-38808000	Flanking Active TSS	Fetal Thymus	thymus
12	chr19:38806800-38808200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr19:38806800-38808200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr19:38806800-38808200	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr19:38806800-38808200	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr19:38806800-38808200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr19:38806800-38808200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr19:38806800-38808200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:38806800-38808200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr19:38806800-38808200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr19:38806800-38808200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:38806800-38808200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr19:38806800-38808200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:38806800-38808200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38806800-38808400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr19:38807000-38807600	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr19:38807000-38807600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr19:38807000-38807800	Weak transcription	Esophagus	oesophagus
29	chr19:38807000-38808000	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr19:38807000-38808200	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr19:38807000-38808200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:38807000-38808200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr19:38807000-38808200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr19:38807000-38808200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:38807000-38808200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:38807000-38808400	Flanking Active TSS	K562	blood
37	chr19:38807000-38809800	Weak transcription	Gastric	stomach
38	chr19:38807000-38809800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:38807000-38810000	Weak transcription	HSMMtube	muscle
40	chr19:38807200-38807600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:38807200-38807600	Enhancers	Fetal Brain Male	brain
42	chr19:38807200-38807600	Enhancers	Placenta	Placenta
43	chr19:38807200-38807600	Enhancers	Spleen	Spleen
44	chr19:38807200-38807800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr19:38807200-38807800	Enhancers	HMEC	breast
46	chr19:38807200-38808000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr19:38807200-38808000	Enhancers	Fetal Stomach	stomach
48	chr19:38807200-38808000	Enhancers	Lung	lung
49	chr19:38807200-38808000	Enhancers	Psoas Muscle	Psoas
50	chr19:38807200-38808000	Enhancers	Right Ventricle	heart

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