Variant report

Variant	rs3859190
Chromosome Location	chr17:38136562-38136563
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:325)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:325 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr17:38136389-38137352	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:38136469-38137473	Gliobla	brain:	n/a	n/a
3	POLR2A	chr17:38136162-38138075	K562	blood:	n/a	n/a
4	POLR2A	chr17:38136478-38136818	GM12878	blood:	n/a	n/a
5	BRCA1	chr17:38136313-38137155	HepG2	liver:	n/a	n/a
6	E2F6	chr17:38136371-38137460	A549	lung:	n/a	chr17:38136759-38136768 chr17:38136761-38136770
7	HCFC1	chr17:38136233-38137345	K562	blood:	n/a	n/a
8	EP300	chr17:38136537-38137215	T-47D	breast:	n/a	chr17:38137006-38137020
9	RCOR1	chr17:38135829-38137232	K562	blood:	n/a	n/a
10	CHD2	chr17:38136168-38137298	K562	blood:	n/a	n/a
11	POLR2A	chr17:38136117-38137643	H1-neurons	neurons:	n/a	n/a
12	NR2C2	chr17:38136562-38137298	Hela-S3	cervix:	n/a	n/a
13	GTF2F1	chr17:38136561-38137240	K562	blood:	n/a	n/a
14	MAZ	chr17:38136276-38137351	GM12878	blood:	n/a	chr17:38137181-38137191
15	RAD21	chr17:38136467-38137174	SK-N-SH_RA	brain:	n/a	n/a
16	EP300	chr17:38136505-38137533	ECC-1	luminal epithelium:	n/a	chr17:38137006-38137020
17	SP1	chr17:38136064-38137478	A549	lung:	n/a	chr17:38136975-38136989
18	SIX5	chr17:38136486-38137304	A549	lung:	n/a	n/a
19	RELA	chr17:38136516-38137278	GM19099	blood:	n/a	n/a
20	TRIM28	chr17:38136538-38137450	K562	blood:	n/a	n/a
21	MAX	chr17:38136410-38137566	ECC-1	luminal epithelium:	n/a	chr17:38137181-38137191
22	SIN3AK20	chr17:38136102-38137642	A549	lung:	n/a	n/a
23	POLR2A	chr17:38136331-38137912	PFSK-1	brain:	n/a	n/a
24	MXI1	chr17:38136537-38137559	HepG2	liver:	n/a	n/a
25	POLR2A	chr17:38136432-38137344	HCT-116	colon:	n/a	n/a
26	WRNIP1	chr17:38136184-38137188	GM12878	blood:	n/a	n/a
27	POLR2A	chr17:38136425-38137360	HEK293	kidney:	n/a	n/a
28	YY1	chr17:38136475-38137344	K562	blood:	n/a	n/a
29	TAF1	chr17:38136521-38137602	HepG2	liver:	n/a	n/a
30	ZBTB7A	chr17:38136092-38137214	K562	blood:	n/a	n/a
31	MXI1	chr17:38136468-38137331	GM12878	blood:	n/a	n/a
32	TAF1	chr17:38136136-38137371	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr17:38136162-38137772	A549	lung:	n/a	chr17:38137181-38137191
34	MAX	chr17:38136254-38137320	GM12878	blood:	n/a	chr17:38137181-38137191
35	RAD21	chr17:38136160-38137069	K562	blood:	n/a	n/a
36	ELF1	chr17:38136377-38137346	A549	lung:	n/a	n/a
37	TBP	chr17:38136120-38137387	K562	blood:	n/a	n/a
38	POLR2A	chr17:38136065-38137537	GM19099	blood:	n/a	n/a
39	YY1	chr17:38136525-38137270	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr17:38136244-38137931	U87	brain:	n/a	n/a
41	USF1	chr17:38136526-38137372	A549	lung:	n/a	n/a
42	TAF1	chr17:38136480-38137378	GM12878	blood:	n/a	n/a
43	SRF	chr17:38136329-38137469	HCT-116	colon:	n/a	n/a
44	POLR2A	chr17:38136447-38137712	ECC-1	luminal epithelium:	n/a	n/a
45	SP1	chr17:38136515-38137266	HepG2	liver:	n/a	chr17:38136975-38136989
46	POLR2A	chr17:38136262-38137925	U87	brain:	n/a	n/a
47	POLR2A	chr17:38136213-38137737	HL-60	blood:	n/a	n/a
48	BACH1	chr17:38136368-38137599	H1-hESC	embryonic stem cell:	n/a	n/a
49	CREB1	chr17:38136487-38137442	ECC-1	luminal epithelium:	n/a	chr17:38136758-38136771
50	REST	chr17:38136255-38137460	HL-60	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38136187..38139299-chr17:38140015..38144342,5	K562	blood:
2	chr17:38136379..38138502-chr17:38148012..38149919,2	K562	blood:
3	chr17:38083515..38085044-chr17:38134757..38136907,2	K562	blood:
4	chr17:38132843..38134558-chr17:38134586..38136777,2	K562	blood:
5	chr17:38073305..38078163-chr17:38135913..38140017,5	K562	blood:
6	chr17:38117802..38119525-chr17:38136512..38138841,3	K562	blood:
7	chr13:33263173..33263826-chr17:38136438..38137035,2	HCT-116	colon:
8	chr17:37822499..37825157-chr17:38134564..38136982,2	K562	blood:
9	chr17:38028703..38029243-chr17:38136410..38137027,2	MCF-7	breast:
10	chr17:38115204..38116742-chr17:38135423..38136956,2	K562	blood:
11	chr17:38136308..38139120-chr17:38254735..38257246,2	MCF-7	breast:
12	chr17:38073305..38078633-chr17:38135671..38140017,6	K562	blood:
13	chr17:38072983..38073973-chr17:38136437..38137023,3	K562	blood:
14	chr17:38063855..38068073-chr17:38135195..38137481,3	K562	blood:
15	chr17:38135295..38137617-chr17:38176453..38178456,2	K562	blood:
16	chr17:37703880..37705005-chr17:38136510..38137377,3	K562	blood:

No data

Variant related genes	Relation type
PSMD3	TF binding region
ENSG00000008838	Chromatin interaction
ENSG00000264968	Chromatin interaction
ENSG00000126368	Chromatin interaction
ENSG00000141744	Chromatin interaction
ENSG00000073605	Chromatin interaction
ENSG00000167914	Chromatin interaction
ENSG00000172057	Chromatin interaction
ENSG00000167258	Chromatin interaction
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1042657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10852937	0.86[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs11652139	1.00[YRI][hapmap]
rs12938879	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[EUR][1000 genomes]
rs2071370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2227324	0.85[EUR][1000 genomes]
rs2227338	0.86[EUR][1000 genomes]
rs2302775	0.86[CHB][hapmap]
rs3816471	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3826330	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3916061	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4082190	0.82[ASN][1000 genomes]
rs4488488	0.82[ASN][1000 genomes]
rs4795411	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4795417	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4795421	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6503532	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8068253	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs921651	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9748108	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9899955	0.86[EUR][1000 genomes]
rs9900199	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9903987	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9905305	0.94[ASN][1000 genomes]
rs9913632	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38135400-38136600	Flanking Active TSS	NH-A	brain
2	chr17:38135400-38136600	Flanking Active TSS	NHEK	skin
3	chr17:38135400-38137800	Active TSS	Duodenum Mucosa	Duodenum
4	chr17:38135600-38136600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr17:38135600-38136600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr17:38135600-38136600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr17:38135600-38136600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr17:38135600-38136600	Flanking Active TSS	Osteobl	bone
9	chr17:38135600-38136800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr17:38135800-38136600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr17:38135800-38136600	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr17:38135800-38136600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr17:38135800-38136600	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr17:38135800-38136600	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr17:38135800-38136600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr17:38135800-38136600	Flanking Active TSS	Dnd41	blood
17	chr17:38135800-38136600	Flanking Active TSS	NHDF-Ad	bronchial
18	chr17:38135800-38136600	Flanking Active TSS	NHLF	lung
19	chr17:38135800-38136800	Flanking Active TSS	HMEC	breast
20	chr17:38136000-38136600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:38136000-38136600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr17:38136000-38136600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr17:38136000-38136600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr17:38136000-38136600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr17:38136000-38136600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr17:38136000-38136600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:38136000-38136600	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr17:38136000-38136600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr17:38136000-38136600	Enhancers	Small Intestine	intestine
30	chr17:38136000-38136600	Flanking Active TSS	Hela-S3	cervix
31	chr17:38136000-38136600	Flanking Active TSS	HSMM	muscle
32	chr17:38136000-38137600	Active TSS	Brain Germinal Matrix	brain
33	chr17:38136000-38137600	Active TSS	Rectal Smooth Muscle	rectum
34	chr17:38136000-38138600	Active TSS	H1 Cell Line	embryonic stem cell
35	chr17:38136200-38136600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr17:38136200-38136600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr17:38136200-38136600	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr17:38136200-38136600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr17:38136200-38136600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr17:38136200-38136600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr17:38136200-38136600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr17:38136200-38136600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr17:38136200-38136600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr17:38136200-38136600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr17:38136200-38136600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr17:38136200-38136600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr17:38136200-38136600	Flanking Active TSS	Liver	Liver
48	chr17:38136200-38136600	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr17:38136200-38136600	Flanking Active TSS	Placenta	Placenta
50	chr17:38136200-38136600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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