Variant report

Variant	rs2055859
Chromosome Location	chr17:37778742-37778743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:37778113-37778788	GM12878	blood:	n/a	n/a
2	JUN	chr17:37778002-37779142	K562	blood:	n/a	chr17:37778170-37778179
3	STAT1	chr17:37778212-37778744	GM12878	blood:	n/a	n/a
4	FOS	chr17:37778686-37778841	MCF10A-Er-Src	breast:	n/a	n/a
5	IRF4	chr17:37778152-37778862	GM12878	blood:	n/a	n/a
6	RAD21	chr17:37778089-37778794	A549	lung:	n/a	chr17:37778182-37778196 chr17:37778233-37778247 chr17:37778289-37778302 chr17:37778208-37778222
7	STAT1	chr17:37778158-37778784	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr17:37777426-37780368	A549	lung:	n/a	chr17:37777636-37777645 chr17:37779850-37779868 chr17:37779852-37779865 chr17:37779851-37779867 chr17:37779845-37779866
9	FOS	chr17:37778578-37778873	MCF10A-Er-Src	breast:	n/a	n/a
10	JUND	chr17:37778197-37778777	HepG2	liver:	n/a	n/a
11	CTCF	chr17:37777934-37778777	HepG2	liver:	n/a	n/a
12	CTCF	chr17:37778660-37778810	GM12867	blood:	n/a	n/a
13	RUNX3	chr17:37778137-37778873	GM12878	blood:	n/a	n/a
14	CREB1	chr17:37778178-37779081	GM12878	blood:	n/a	n/a
15	REST	chr17:37777906-37779008	A549	lung:	n/a	chr17:37777984-37777994
16	RAD21	chr17:37777945-37778867	HCT-116	colon:	n/a	chr17:37778182-37778196 chr17:37778233-37778247 chr17:37778289-37778302 chr17:37778208-37778222
17	ZNF143	chr17:37778153-37778884	GM12878	blood:	n/a	chr17:37778809-37778824
18	NFATC1	chr17:37778139-37778804	GM12878	blood:	n/a	n/a
19	YY1	chr17:37778198-37779076	GM12892	blood:	n/a	n/a
20	SMC3	chr17:37778161-37778846	GM12878	blood:	n/a	chr17:37778263-37778273
21	YY1	chr17:37778617-37778965	GM12878	blood:	n/a	n/a
22	CTCF	chr17:37778016-37778901	K562	blood:	n/a	n/a
23	BATF	chr17:37778574-37778862	GM12878	blood:	n/a	chr17:37778742-37778753
24	ATF3	chr17:37778161-37778758	GM12878	blood:	n/a	n/a
25	CTCF	chr17:37777790-37778865	HepG2	liver:	n/a	n/a
26	STAT5A	chr17:37778172-37778833	GM12878	blood:	n/a	n/a
27	MAX	chr17:37778052-37779048	A549	lung:	n/a	chr17:37778172-37778182 chr17:37778840-37778849
28	CTCF	chr17:37777089-37778956	SK-N-SH	brain:	n/a	chr17:37777636-37777645
29	REST	chr17:37778175-37778769	PANC-1	pancreas:	n/a	n/a
30	TCF12	chr17:37778072-37778809	A549	lung:	n/a	chr17:37778230-37778240 chr17:37778189-37778196 chr17:37778215-37778222
31	SMC3	chr17:37778175-37778763	HepG2	liver:	n/a	chr17:37778263-37778273
32	GTF2F1	chr17:37778700-37778777	K562	blood:	n/a	n/a
33	WRNIP1	chr17:37778170-37778799	GM12878	blood:	n/a	n/a
34	YY1	chr17:37778717-37778929	K562	blood:	n/a	n/a
35	CTCF	chr17:37778720-37778870	AG04450	lung:	n/a	n/a
36	STAT3	chr17:37778253-37778846	MCF10A-Er-Src	breast:	n/a	n/a
37	REST	chr17:37778179-37778756	HL-60	blood:	n/a	n/a
38	FOSL2	chr17:37778100-37778794	A549	lung:	n/a	chr17:37778170-37778179
39	MTA3	chr17:37778080-37778854	GM12878	blood:	n/a	n/a
40	YY1	chr17:37778614-37778978	GM12892	blood:	n/a	n/a
41	CTCF	chr17:37778740-37778890	HRE	kidney:	n/a	n/a
42	RAD21	chr17:37777940-37778948	HCT-116	colon:	n/a	chr17:37778182-37778196 chr17:37778233-37778247 chr17:37778289-37778302 chr17:37778208-37778222
43	MAZ	chr17:37778111-37778792	IMR90	lung:	n/a	chr17:37778172-37778182
44	SMC3	chr17:37777824-37778967	SK-N-SH	brain:	n/a	chr17:37778263-37778273
45	NFIC	chr17:37778258-37778749	GM12878	blood:	n/a	n/a
46	CTCF	chr17:37777787-37778844	K562	blood:	n/a	n/a
47	CTCF	chr17:37777779-37778942	HCT-116	colon:	n/a	n/a
48	CTCF	chr17:37777669-37779081	HCT-116	colon:	n/a	n/a
49	YY1	chr17:37778624-37779029	GM12878	blood:	n/a	n/a
50	BATF	chr17:37778601-37778905	GM12878	blood:	n/a	chr17:37778742-37778753

No.	Distal block	Cell Line	Cell type
1	chr17:37776626..37780124-chr17:37818606..37821377,4	K562	blood:
2	chr17:37703730..37705624-chr17:37777887..37780361,14	K562	blood:
3	chr17:37777309..37780105-chr17:37909118..37911531,3	MCF-7	breast:
4	chr17:37777123..37780362-chr17:37909816..37911514,36	K562	blood:
5	chr17:37777770..37778817-chr17:37910195..37911123,12	MCF-7	breast:
6	chr17:37777435..37780800-chr17:37803920..37808668,4	K562	blood:
7	chr17:37704896..37707478-chr17:37777687..37780191,2	MCF-7	breast:
8	chr17:37777964..37778788-chr17:38020511..38021070,2	MCF-7	breast:
9	chr17:37777756..37783081-chr17:37819129..37825010,9	K562	blood:
10	chr17:37778256..37779018-chr17:37791676..37792248,2	K562	blood:
11	chr17:37776845..37781693-chr17:37790426..37796554,9	K562	blood:
12	chr17:37777900..37778761-chr17:37991112..37991981,2	K562	blood:
13	chr11:119227095..119227706-chr17:37778289..37778824,2	MCF-7	breast:
14	chr17:37769208..37773729-chr17:37777189..37781252,6	K562	blood:
15	chr17:37778246..37778910-chr17:37874656..37875550,3	MCF-7	breast:
16	chr17:37778539..37780288-chr17:37893179..37895344,2	K562	blood:
17	chr17:37777901..37778833-chr17:37828093..37829149,5	MCF-7	breast:
18	chr17:37703733..37704728-chr17:37776531..37778900,10	MCF-7	breast:
19	chr17:37777977..37778882-chr17:37886248..37887317,3	K562	blood:
20	chr17:37778015..37778817-chr17:38136400..38137216,2	MCF-7	breast:
21	chr17:37778202..37782049-chr17:37783082..37786622,6	K562	blood:
22	chr17:37778262..37779269-chr17:37908489..37909454,3	K562	blood:
23	chr17:37777863..37778860-chr17:37824368..37824901,3	K562	blood:
24	chr17:37778310..37780085-chr17:37905969..37908685,2	K562	blood:
25	chr17:37706868..37707410-chr17:37778327..37778844,2	MCF-7	breast:
26	chr17:37777847..37779169-chr17:37827001..37829318,18	K562	blood:
27	chr17:37777961..37778768-chr17:37910171..37911038,7	MCF-7	breast:
28	chr17:37777903..37778847-chr17:37809797..37810807,7	K562	blood:
29	chr17:37777860..37778748-chr17:37793007..37793767,3	K562	blood:
30	chr17:37775807..37781695-chr17:37822673..37828377,10	K562	blood:
31	chr17:37778209..37778847-chr17:37843626..37844457,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC087491.2.1-1	chr17:37778329-37778766	ENSG00000214546.3

Variant related genes	Relation type
PPP1R1B	TF binding region
ENSG00000141736	Chromatin interaction
ENSG00000167258	Chromatin interaction
ENSG00000173991	Chromatin interaction
ENSG00000131748	Chromatin interaction
ENSG00000108344	Chromatin interaction
ENSG00000161395	Chromatin interaction
ENSG00000141744	Chromatin interaction
ENSG00000141738	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000131771	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12937003	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12942857	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12943875	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2132140	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs33932099	0.92[AFR][1000 genomes]
rs34130088	0.98[AFR][1000 genomes]
rs34445181	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34963535	1.00[EUR][1000 genomes]
rs57837184	1.00[EUR][1000 genomes]
rs59438000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67615144	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68087665	1.00[EUR][1000 genomes]
rs71369780	0.87[AFR][1000 genomes]
rs7224588	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73308326	1.00[EUR][1000 genomes]
rs7503843	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8066399	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8075130	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8075931	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
3	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
4	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
5	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	nsv908208	chr17:37749259-37781849	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv908209	chr17:37749259-37790340	Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv908210	chr17:37761202-37781849	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv908211	chr17:37765047-37782410	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv908212	chr17:37765047-37790340	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv457738	chr17:37770005-37831035	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv574991	chr17:37770005-37831035	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37775000-37779400	Weak transcription	Left Ventricle	heart
2	chr17:37775000-37782400	Weak transcription	Gastric	stomach
3	chr17:37775200-37779600	Weak transcription	Spleen	Spleen
4	chr17:37775200-37781200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:37775200-37782600	Weak transcription	Lung	lung
6	chr17:37775200-37782800	Weak transcription	Right Atrium	heart
7	chr17:37775400-37779400	Weak transcription	HMEC	breast
8	chr17:37775400-37782800	Weak transcription	Right Ventricle	heart
9	chr17:37775600-37779400	Weak transcription	Colonic Mucosa	Colon
10	chr17:37777200-37779000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr17:37777200-37781200	Enhancers	Fetal Brain Male	brain
12	chr17:37777400-37780200	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr17:37777800-37778800	Bivalent Enhancer	Fetal Stomach	stomach
14	chr17:37777800-37779000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:37777800-37779400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:37777800-37780200	Enhancers	Primary B cells from peripheral blood	blood
17	chr17:37777800-37780400	Enhancers	Primary B cells from cord blood	blood
18	chr17:37778000-37778800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr17:37778000-37778800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr17:37778000-37779000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr17:37778000-37779000	Enhancers	Fetal Intestine Large	intestine
22	chr17:37778000-37779800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr17:37778000-37780200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr17:37778000-37780200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr17:37778000-37780200	Enhancers	Adipose Nuclei	Adipose
26	chr17:37778000-37780200	Enhancers	Fetal Intestine Small	intestine
27	chr17:37778000-37780400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr17:37778200-37778800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:37778200-37780000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:37778200-37780000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:37778200-37780000	Enhancers	Fetal Thymus	thymus
32	chr17:37778200-37780200	Enhancers	Brain Germinal Matrix	brain
33	chr17:37778200-37780200	Enhancers	Dnd41	blood
34	chr17:37778400-37778800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
35	chr17:37778400-37778800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:37778400-37778800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr17:37778400-37778800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
38	chr17:37778400-37778800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
39	chr17:37778400-37778800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr17:37778400-37778800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
41	chr17:37778400-37778800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr17:37778400-37778800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr17:37778400-37778800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr17:37778400-37778800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr17:37778400-37778800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr17:37778400-37778800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr17:37778400-37778800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr17:37778400-37778800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr17:37778400-37778800	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr17:37778400-37778800	Flanking Active TSS	Duodenum Mucosa	Duodenum

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