Variant report

Variant	rs4988344
Chromosome Location	chr17:59924612-59924613
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59924200..59926271-chr17:62493246..62495056,2	MCF-7	breast:
2	chr17:59922631..59924965-chr20:55840316..55842236,2	MCF-7	breast:
3	chr17:59922834..59925461-chr20:55688091..55690471,2	MCF-7	breast:
4	chr17:59924478..59926464-chr17:59949520..59951660,2	K562	blood:
5	chr17:59923295..59925454-chr3:76423804..76426584,2	MCF-7	breast:
6	chr17:59922882..59925305-chr20:55682446..55685086,2	MCF-7	breast:
7	chr17:59923631..59927756-chr20:55841181..55844578,4	MCF-7	breast:
8	chr17:58758381..58760756-chr17:59924368..59926184,2	MCF-7	breast:
9	chr17:59923118..59924764-chr17:59928753..59930599,2	K562	blood:
10	chr17:59754561..59757250-chr17:59924100..59926334,2	MCF-7	breast:
11	chr17:59922363..59930982-chr17:59932743..59942161,16	K562	blood:
12	chr17:59923027..59925292-chr20:60641069..60642789,2	MCF-7	breast:
13	chr17:59923960..59927363-chr20:60638070..60642811,4	MCF-7	breast:
14	chr17:59922988..59926695-chr17:59932114..59939260,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000202361	Chromatin interaction
ENSG00000265306	Chromatin interaction
ENSG00000203266	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000130699	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10512492	0.90[CEU][hapmap]
rs12451910	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12452094	0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12452732	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12453644	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12600909	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12601269	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12604037	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs16945692	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16945753	0.91[CEU][hapmap];0.87[YRI][hapmap]
rs16945759	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs16945801	0.90[CEU][hapmap];0.85[YRI][hapmap]
rs2271576	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2378908	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs3744434	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4968408	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4968451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968452	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968454	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4968455	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4968456	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4968457	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968460	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes]
rs4968461	0.91[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs4968462	0.87[YRI][hapmap]
rs56794817	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58624595	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59080342	0.84[AMR][1000 genomes]
rs61169879	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61658218	0.83[AMR][1000 genomes]
rs7218724	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs7221089	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs73332565	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73332580	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73332598	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73334621	0.83[AMR][1000 genomes]
rs8065778	0.91[CEU][hapmap];0.87[YRI][hapmap]
rs8066964	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs8074890	0.91[CEU][hapmap];0.87[YRI][hapmap]
rs8080599	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8081917	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9630735	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9630736	0.90[CEU][hapmap];0.87[YRI][hapmap]

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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
3	nsv575842	chr17:59812748-59927307	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
4	nsv908675	chr17:59835864-59937286	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
5	nsv575843	chr17:59869081-59935723	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59863600-59925000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:59870400-59933400	Weak transcription	Fetal Intestine Large	intestine
3	chr17:59884200-59933200	Weak transcription	K562	blood
4	chr17:59898800-59939600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr17:59898800-59939800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:59904200-59927000	Weak transcription	Fetal Kidney	kidney
7	chr17:59904800-59933200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr17:59905400-59931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr17:59905800-59939000	Weak transcription	Primary T cells from cord blood	blood
10	chr17:59906200-59940200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:59911600-59937800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr17:59911800-59939000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:59912000-59925600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:59912000-59938400	Weak transcription	HUVEC	blood vessel
15	chr17:59912200-59939200	Weak transcription	HSMM	muscle
16	chr17:59912200-59939800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr17:59912400-59931400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:59912400-59931400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:59912400-59938600	Weak transcription	NHDF-Ad	bronchial
20	chr17:59912400-59938600	Weak transcription	NHEK	skin
21	chr17:59912400-59939400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr17:59912400-59940000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:59912400-59940400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr17:59914600-59932600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:59914600-59938600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr17:59916400-59931400	Strong transcription	Dnd41	blood
27	chr17:59916600-59938600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr17:59917400-59925800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:59917800-59939200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr17:59918000-59939000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr17:59918800-59927400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr17:59919200-59924800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr17:59919200-59925400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:59919200-59927400	Strong transcription	A549	lung
35	chr17:59919200-59928000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr17:59919200-59928000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:59919400-59928400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr17:59919800-59934600	Weak transcription	Ovary	ovary
39	chr17:59920400-59940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr17:59920600-59925800	Strong transcription	HepG2	liver
41	chr17:59920600-59927000	Weak transcription	Fetal Lung	lung
42	chr17:59920600-59930600	Strong transcription	Fetal Thymus	thymus
43	chr17:59921200-59939800	Weak transcription	Thymus	Thymus
44	chr17:59921600-59927400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr17:59921600-59940000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr17:59922000-59926400	Weak transcription	Fetal Intestine Small	intestine
47	chr17:59922000-59937800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr17:59922200-59933000	Weak transcription	HMEC	breast
49	chr17:59922200-59938400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:59922200-59939000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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