Variant report

Variant	rs7220419
Chromosome Location	chr17:45908405-45908406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:316)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:316 , 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	POLR2A	chr17:45908385-45909213	HUVEC	blood vessel:	n/a	n/a
2	TBP	chr17:45908188-45909086	K562	blood:	n/a	n/a
3	GABPA	chr17:45908191-45909249	SK-N-SH	brain:	n/a	chr17:45908990-45909001 chr17:45908992-45909001
4	SP1	chr17:45908240-45909277	A549	lung:	n/a	n/a
5	CTCF	chr17:45908360-45908510	NB4	blood:	n/a	n/a
6	TAF1	chr17:45908344-45909243	A549	lung:	n/a	n/a
7	CTCF	chr17:45908340-45908490	AG10803	skin:	n/a	n/a
8	CTCF	chr17:45908360-45908510	Caco-2	colon:	n/a	n/a
9	POLR2A	chr17:45908072-45909094	K562	blood:	n/a	n/a
10	CTCF	chr17:45908340-45908490	GM12872	blood:	n/a	n/a
11	POLR2A	chr17:45908336-45909207	PFSK-1	brain:	n/a	n/a
12	MYC	chr17:45908227-45909156	K562	blood:	n/a	n/a
13	CTCF	chr17:45908280-45908430	A549	lung:	n/a	n/a
14	POLR2A	chr17:45908339-45909158	K562	blood:	n/a	n/a
15	IRF1	chr17:45908290-45909245	K562	blood:	n/a	n/a
16	RUNX3	chr17:45908317-45909189	GM12878	blood:	n/a	n/a
17	CEBPB	chr17:45908316-45909434	GM12878	blood:	n/a	n/a
18	CTCF	chr17:45908260-45908410	HFF-Myc	foreskin:	n/a	n/a
19	CTCF	chr17:45908360-45908510	HRE	kidney:	n/a	n/a
20	FOXA2	chr17:45908233-45908569	HepG2	liver:	n/a	n/a
21	POLR2A	chr17:45908058-45909209	K562	blood:	n/a	n/a
22	CTCF	chr17:45908360-45908510	HUVEC	blood vessel:	n/a	n/a
23	YY1	chr17:45908354-45909130	ECC-1	luminal epithelium:	n/a	n/a
24	USF2	chr17:45908269-45909057	HepG2	liver:	n/a	n/a
25	MAX	chr17:45908286-45909242	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr17:45908360-45908510	GM12875	blood:	n/a	n/a
27	PML	chr17:45908246-45909259	GM12878	blood:	n/a	n/a
28	POLR2A	chr17:45908346-45909248	Raji	blood:	n/a	n/a
29	POLR2A	chr17:45908093-45909317	SK-N-SH	brain:	n/a	n/a
30	CTCF	chr17:45908380-45908530	HRPEpiC	eye:	n/a	n/a
31	CTCF	chr17:45907957-45909747	A549	lung:	n/a	n/a
32	POLR2A	chr17:45908190-45909281	HepG2	liver:	n/a	n/a
33	POLR2A	chr17:45908333-45909618	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr17:45908300-45908450	HL-60	blood:	n/a	n/a
35	GABPA	chr17:45908179-45909584	SK-N-SH	brain:	n/a	chr17:45908990-45909001 chr17:45908992-45909001
36	CTCF	chr17:45908280-45908430	HMEC	breast:	n/a	n/a
37	MAX	chr17:45908209-45909195	MCF-7	breast:	n/a	n/a
38	POLR2A	chr17:45908296-45909247	GM12891	blood:	n/a	n/a
39	POLR2A	chr17:45908325-45909316	GM12892	blood:	n/a	n/a
40	RAD21	chr17:45908348-45908550	GM12878	blood:	n/a	n/a
41	CTCF	chr17:45908320-45908470	HFF	foreskin:	n/a	n/a
42	CTCF	chr17:45908360-45908510	GM12864	blood:	n/a	n/a
43	CTCF	chr17:45908380-45908530	GM12865	blood:	n/a	n/a
44	MXI1	chr17:45908366-45909255	K562	blood:	n/a	n/a
45	RAD21	chr17:45908281-45908567	SK-N-SH_RA	brain:	n/a	n/a
46	CTCF	chr17:45908340-45908490	AoAF	blood vessel:	n/a	n/a
47	JUND	chr17:45908317-45908805	HepG2	liver:	n/a	n/a
48	CTCF	chr17:45908360-45908510	HA-sp	spinal cord:	n/a	n/a
49	POLR2A	chr17:45908286-45909203	H1-neurons	neurons:	n/a	n/a
50	CTCF	chr17:45908360-45908510	NHEK	skin:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45908091..45909989-chr17:45932469..45934712,2	K562	blood:
2	chr17:45907498..45909861-chr17:45916216..45917789,2	K562	blood:
3	chr17:45907387..45909991-chr17:45928355..45930503,2	MCF-7	breast:
4	chr17:45906763..45908800-chr17:45971600..45974534,3	MCF-7	breast:
5	chr17:45769943..45772007-chr17:45907461..45910429,3	K562	blood:
6	chr17:45908246..45910427-chr17:45971152..45975040,4	K562	blood:
7	chr17:45906214..45908869-chr17:46017254..46019863,3	MCF-7	breast:
8	chr17:45907261..45910696-chr17:45969933..45974046,5	MCF-7	breast:
9	chr17:45894310..45903569-chr17:45906761..45911816,14	MCF-7	breast:
10	chr17:45726797..45728320-chr17:45906993..45909884,2	MCF-7	breast:

No data

Variant related genes	Relation type
LRRC46	TF binding region
MRPL10	TF binding region
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000006025	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000198933	Chromatin interaction
ENSG00000141295	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1008934	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11079804	0.94[MEX][hapmap]
rs11545723	0.88[MEX][hapmap]
rs11869958	0.80[CHB][hapmap]
rs11870002	0.81[CHB][hapmap]
rs12452082	1.00[MEX][hapmap]
rs12452366	0.80[ASN][1000 genomes]
rs1985407	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs2023799	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35598018	0.80[ASN][1000 genomes]
rs4362431	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs4793734	0.88[MEX][hapmap]
rs4794225	0.94[MEX][hapmap]
rs6503871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757061	0.85[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8079715	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs878171	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs9674817	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs9904820	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs9907142	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs991108	0.82[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs9914156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 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	chr17:45907200-45909600	Flanking Active TSS	Duodenum Mucosa	Duodenum
2	chr17:45907400-45908600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr17:45907400-45908600	Flanking Active TSS	Dnd41	blood
4	chr17:45907600-45908600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr17:45907600-45908600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr17:45907600-45908600	Flanking Active TSS	Osteobl	bone
7	chr17:45907600-45908800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:45907600-45909200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr17:45907600-45909200	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr17:45907600-45909400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr17:45907600-45909400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:45907600-45909600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr17:45907600-45909800	Flanking Active TSS	Liver	Liver
14	chr17:45907800-45908600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr17:45907800-45908600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr17:45907800-45909200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr17:45907800-45909200	Active TSS	A549	lung
18	chr17:45907800-45909200	Active TSS	GM12878-XiMat	blood
19	chr17:45907800-45909200	Active TSS	K562	blood
20	chr17:45907800-45909600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr17:45908000-45908600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:45908000-45908600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr17:45908000-45908600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr17:45908000-45908600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr17:45908000-45908600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr17:45908000-45908600	Flanking Active TSS	Brain Angular Gyrus	brain
27	chr17:45908000-45908600	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr17:45908000-45908600	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr17:45908000-45908600	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr17:45908000-45908600	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr17:45908000-45908600	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr17:45908000-45908600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr17:45908000-45908600	Flanking Active TSS	Fetal Brain Female	brain
34	chr17:45908000-45908600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr17:45908000-45908600	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr17:45908000-45908600	Flanking Active TSS	Placenta	Placenta
37	chr17:45908000-45908600	Flanking Active TSS	Fetal Stomach	stomach
38	chr17:45908000-45908600	Flanking Active TSS	Fetal Thymus	thymus
39	chr17:45908000-45908600	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr17:45908000-45909200	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr17:45908000-45909200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr17:45908000-45909200	Transcr. at gene 5' and 3'	Right Atrium	heart
43	chr17:45908000-45909200	Active TSS	Right Ventricle	heart
44	chr17:45908000-45909200	Active TSS	NHDF-Ad	bronchial
45	chr17:45908000-45909400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr17:45908000-45909400	Active TSS	H9 Cell Line	embryonic stem cell
47	chr17:45908000-45909400	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr17:45908000-45909400	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr17:45908000-45909400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr17:45908000-45909600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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