Variant report

Variant	rs28653561
Chromosome Location	chr17:19911828-19911829
allele	C/G
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	MAZ	chr17:19911800-19912900	IMR90	lung:	n/a	chr17:19912536-19912546
2	CTCF	chr17:19911823-19912232	H1-hESC	embryonic stem cell:	n/a	chr17:19912019-19912028
3	CTCF	chr17:19911508-19914638	A549	lung:	n/a	chr17:19912622-19912631 chr17:19912985-19912998 chr17:19912998-19913011 chr17:19912617-19912633 chr17:19912019-19912028 chr17:19912619-19912629 chr17:19912616-19912634
4	REST	chr17:19911784-19914244	A549	lung:	n/a	chr17:19912120-19912133 chr17:19913349-19913362 chr17:19913340-19913353
5	POLR2A	chr17:19911794-19911880	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chr17:19911526-19914125	A549	lung:	n/a	n/a
7	FOXA2	chr17:19911731-19912954	A549	lung:	n/a	n/a
8	WRNIP1	chr17:19911748-19911937	GM12878	blood:	n/a	n/a
9	ZNF263	chr17:19911453-19914279	HEK293-T-REx	kidney:	n/a	chr17:19913782-19913791 chr17:19913411-19913420 chr17:19913012-19913021 chr17:19913789-19913798
10	MAX	chr17:19911673-19913844	A549	lung:	n/a	chr17:19912536-19912546
11	BCL3	chr17:19911733-19912969	A549	lung:	n/a	chr17:19912204-19912213 chr17:19912537-19912550 chr17:19912089-19912098
12	FOXA2	chr17:19911747-19912281	A549	lung:	n/a	n/a
13	SP1	chr17:19911808-19912869	A549	lung:	n/a	chr17:19912136-19912145 chr17:19912137-19912146 chr17:19912135-19912147 chr17:19912135-19912147
14	E2F6	chr17:19911763-19913780	A549	lung:	n/a	chr17:19913343-19913353 chr17:19912136-19912145
15	MAX	chr17:19911533-19914165	A549	lung:	n/a	chr17:19912536-19912546
16	SIN3A	chr17:19911733-19913865	H1-hESC	embryonic stem cell:	n/a	chr17:19913343-19913356
17	CTCF	chr17:19911743-19914016	SK-N-SH	brain:	n/a	chr17:19912622-19912631 chr17:19912985-19912998 chr17:19912998-19913011 chr17:19912617-19912633 chr17:19912019-19912028 chr17:19912619-19912629 chr17:19912616-19912634
18	HCFC1	chr17:19911771-19914635	Hela-S3	cervix:	n/a	n/a
19	KAP1	chr17:19911800-19912785	U2OS	brain:	n/a	n/a
20	KAP1	chr17:19911720-19914314	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19770311..19771954-chr17:19910328..19912594,2	MCF-7	breast:
2	chr17:19879148..19882537-chr17:19911149..19913260,3	MCF-7	breast:
3	chr17:19879669..19882225-chr17:19910498..19912176,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKAP10-1	chr17:19911364-19912547	ENSG00000261033.1
2	lnc-AKAP10-1	chr17:19911368-19912547	NONHSAT146538

Variant related genes	Relation type
SPECC1	TF binding region
ENSG00000108599	Chromatin interaction
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11867646	0.81[ASN][1000 genomes]
rs11867652	0.81[ASN][1000 genomes]
rs16960545	1.00[EUR][1000 genomes]
rs16960602	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28410781	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28424266	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28581607	1.00[EUR][1000 genomes]
rs28713561	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28767032	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28830504	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28865331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909257	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6587207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587208	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6587212	0.90[ASN][1000 genomes]
rs7207459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207702	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7208033	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7210076	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7210751	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7214107	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7215639	1.00[EUR][1000 genomes]
rs7215769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7217387	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7217862	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7217868	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7217928	1.00[EUR][1000 genomes]
rs7218251	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7218919	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7219153	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7219487	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7219688	0.81[ASN][1000 genomes]
rs7220490	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7221669	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7223323	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7224373	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7224419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224713	1.00[EUR][1000 genomes]
rs7224875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065122	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068015	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068488	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8071670	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8079093	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079487	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8080190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8082671	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9889938	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9890105	1.00[AMR][1000 genomes]
rs9891008	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9892175	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9892271	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9893185	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9893296	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9894666	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9895556	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9896010	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9896387	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9896499	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896633	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9896641	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9897430	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9897607	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9898618	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9900393	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9900441	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9900510	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9901862	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9902663	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903631	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9904059	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9908415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909011	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9909012	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9909242	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9909544	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9911408	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9911872	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9912184	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9912648	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9912657	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9913858	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914328	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9914429	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9915039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915413	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3382860	chr17:19894909-19918588	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19911400-19912000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr17:19911400-19912000	Bivalent Enhancer	Primary T cells from cord blood	blood
3	chr17:19911400-19912200	Flanking Active TSS	A549	lung
4	chr17:19911600-19912000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
5	chr17:19911600-19912000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr17:19911600-19912000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:19911600-19913600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr17:19911600-19913800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr17:19911800-19912000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
10	chr17:19911800-19912000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:19911800-19912000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr17:19911800-19912000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:19911800-19912000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
14	chr17:19911800-19912000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
15	chr17:19911800-19912000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:19911800-19912000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:19911800-19912000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr17:19911800-19912000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr17:19911800-19912000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
20	chr17:19911800-19912000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr17:19911800-19912000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr17:19911800-19912000	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
23	chr17:19911800-19912000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr17:19911800-19912000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr17:19911800-19912000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr17:19911800-19912000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:19911800-19912000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
28	chr17:19911800-19912000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
29	chr17:19911800-19912000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
30	chr17:19911800-19912000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:19911800-19912000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:19911800-19912000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr17:19911800-19912000	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
34	chr17:19911800-19912000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:19911800-19912000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
36	chr17:19911800-19912000	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
37	chr17:19911800-19912000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:19911800-19912000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:19911800-19912000	Enhancers	Adipose Nuclei	Adipose
40	chr17:19911800-19912000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr17:19911800-19912000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
42	chr17:19911800-19912000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr17:19911800-19912000	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr17:19911800-19912000	Bivalent Enhancer	Fetal Stomach	stomach
45	chr17:19911800-19912000	Bivalent Enhancer	Fetal Thymus	thymus
46	chr17:19911800-19912000	Enhancers	Gastric	stomach
47	chr17:19911800-19912000	Enhancers	Left Ventricle	heart
48	chr17:19911800-19912000	Enhancers	Pancreas	Pancrea
49	chr17:19911800-19912000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
50	chr17:19911800-19912000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle

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