Variant report

Variant	rs2983715
Chromosome Location	chr1:45186056-45186057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:61)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr1:45186006-45186343	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:45185998-45186104	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:45186028-45186380	HepG2	liver:	n/a	n/a
4	FOXA2	chr1:45185983-45186228	HepG2	liver:	n/a	n/a
5	FOXA1	chr1:45186032-45186294	T-47D	breast:	n/a	n/a
6	FOXA1	chr1:45186037-45186264	T-47D	breast:	n/a	n/a
7	USF2	chr1:45185991-45186291	K562	blood:	n/a	n/a
8	CTCF	chr1:45185920-45186070	HepG2	liver:	n/a	n/a
9	HEY1	chr1:45185789-45186545	K562	blood:	n/a	n/a
10	FOXA1	chr1:45186017-45186375	HepG2	liver:	n/a	n/a

No data

(count:61 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr1:45185360..45189158-chr1:210547543..210549064,10	K562	blood:
2	chr1:45126820..45128674-chr1:45185571..45187169,2	MCF-7	breast:
3	chr1:45185377..45188266-chr12:102512254..102513821,2	MCF-7	breast:
4	chr1:45184531..45187337-chr1:45484420..45488341,4	K562	blood:
5	chr1:45184334..45189303-chr1:45475138..45480545,18	K562	blood:
6	chr1:45185746..45188870-chr1:45307191..45310438,4	K562	blood:
7	chr1:45184920..45187380-chr1:46595320..46596942,2	K562	blood:
8	chr1:45184712..45189957-chr1:45986029..45989344,7	K562	blood:
9	chr1:45095364..45099259-chr1:45185766..45189852,13	K562	blood:
10	chr1:45111755..45115148-chr1:45184742..45187156,4	K562	blood:
11	chr1:44990153..44991798-chr1:45185234..45187477,2	K562	blood:
12	chr1:45185419..45187569-chr19:13261567..13264440,2	K562	blood:
13	chr1:45185969..45188598-chr1:45964540..45967567,4	K562	blood:
14	chr1:45185754..45187905-chr1:46712528..46714563,2	K562	blood:
15	chr1:44479434..44482255-chr1:45185204..45188924,4	K562	blood:
16	chr1:45184834..45186919-chr19:13262940..13265766,2	K562	blood:
17	chr1:45119430..45122212-chr1:45185385..45187031,2	MCF-7	breast:
18	chr1:45185461..45187153-chr1:45217783..45220388,2	MCF-7	breast:
19	chr1:45179633..45191596-chr1:45283435..45288613,20	MCF-7	breast:
20	chr1:45185285..45189072-chr1:45803209..45809453,10	K562	blood:
21	chr1:45108036..45110082-chr1:45185461..45187287,3	K562	blood:
22	chr1:45184765..45187186-chr17:56706793..56709257,2	K562	blood:
23	chr1:45185509..45188442-chr1:45240940..45242560,2	MCF-7	breast:
24	chr1:45100500..45107773-chr1:45184365..45188884,11	K562	blood:
25	chr1:45086647..45106769-chr1:45179099..45192041,56	K562	blood:
26	chr1:45185144..45187303-chr1:45450829..45452396,3	MCF-7	breast:
27	chr1:45183934..45186211-chr1:45344753..45346709,2	K562	blood:
28	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
29	chr1:45185979..45188914-chr1:45226939..45229807,2	MCF-7	breast:
30	chr1:45185720..45187658-chr1:45273782..45275923,3	MCF-7	breast:
31	chr1:45185476..45188775-chr1:46033224..46037144,6	K562	blood:
32	chr1:45185787..45187387-chr1:47798455..47800137,2	K562	blood:
33	chr1:45185937..45187486-chr1:46057167..46058837,2	K562	blood:
34	chr1:45183882..45187540-chr1:45263145..45267405,5	MCF-7	breast:
35	chr1:45185248..45187840-chr6:26198016..26200996,2	K562	blood:
36	chr1:45184864..45189212-chr1:45804136..45808316,8	K562	blood:
37	chr1:45135137..45136656-chr1:45184445..45187267,2	MCF-7	breast:
38	chr1:45183794..45190315-chr1:45281186..45287888,32	MCF-7	breast:
39	chr1:45184459..45186748-chr1:46076080..46077927,2	K562	blood:
40	chr1:11968288..11970254-chr1:45185692..45188658,3	K562	blood:
41	chr1:44411034..44414145-chr1:45184783..45188657,3	K562	blood:
42	chr1:45185676..45189343-chr1:46151396..46155571,4	K562	blood:
43	chr1:44511476..44514442-chr1:45185568..45187160,2	K562	blood:
44	chr1:45183375..45186352-chr1:45956867..45960308,3	K562	blood:
45	chr1:45185596..45187362-chr1:45255952..45259330,3	MCF-7	breast:
46	chr1:45185476..45187340-chr1:46034490..46036122,2	K562	blood:
47	chr1:45184399..45189674-chr1:45270870..45279135,15	MCF-7	breast:
48	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:
49	chr1:45185888..45187495-chr9:93118658..93120159,2	K562	blood:
50	chr1:45186012..45189065-chr1:45262922..45268915,8	MCF-7	breast:

No data

Variant related genes	Relation type
C1orf228	TF binding region
ENSG00000236624	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000226499	Chromatin interaction
ENSG00000162368	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000267598	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000160888	Chromatin interaction
ENSG00000201801	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000230615	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000196517	Chromatin interaction
ENSG00000137504	Chromatin interaction
ENSG00000237950	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000117408	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000187147	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000075188	Chromatin interaction
ENSG00000095066	Chromatin interaction
ENSG00000132773	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11211046	0.82[JPT][hapmap]
rs12059964	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs12407627	0.94[CEU][hapmap]
rs17391430	0.94[CEU][hapmap]
rs263965	0.82[JPT][hapmap]
rs263975	0.82[JPT][hapmap]
rs3795712	0.94[CEU][hapmap]
rs3795715	0.94[CEU][hapmap]
rs4542248	0.82[ASN][1000 genomes]
rs6429548	0.93[CHD][hapmap];0.87[JPT][hapmap]
rs746320	0.82[JPT][hapmap]
rs7524446	0.86[ASN][1000 genomes]
rs7526786	0.82[JPT][hapmap]
rs9988451	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
6	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
7	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2983715	NASP	cis	cerebellum	SCAN
rs2983715	CDC20	cis	cerebellum	SCAN
rs2983715	C1orf84	cis	parietal	SCAN
rs2983715	LEPRE1	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45174400-45190400	Weak transcription	Lung	lung
2	chr1:45180800-45187200	Weak transcription	Right Atrium	heart
3	chr1:45181000-45187800	Weak transcription	Placenta	Placenta
4	chr1:45181200-45186800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:45181200-45186800	Weak transcription	A549	lung
6	chr1:45181200-45187000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:45181200-45187200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:45181200-45188800	Weak transcription	Liver	Liver
9	chr1:45181200-45194800	Weak transcription	Brain Anterior Caudate	brain
10	chr1:45182800-45186800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:45183000-45187200	Enhancers	Primary T cells fromperipheralblood	blood
12	chr1:45183000-45187600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr1:45183000-45188800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:45183000-45188800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:45183200-45187400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:45183200-45189000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr1:45183800-45186200	Enhancers	Spleen	Spleen
18	chr1:45184000-45187800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:45184000-45189000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:45184000-45189200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:45184000-45191000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:45184200-45186800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:45184200-45188200	Weak transcription	Colonic Mucosa	Colon
24	chr1:45184200-45188800	Enhancers	GM12878-XiMat	blood
25	chr1:45184400-45187600	Enhancers	K562	blood
26	chr1:45184600-45186800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr1:45184600-45188800	Enhancers	Primary T cells from cord blood	blood
28	chr1:45184600-45189000	Enhancers	Fetal Thymus	thymus
29	chr1:45184800-45187200	Enhancers	Thymus	Thymus
30	chr1:45184800-45188800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:45184800-45188800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:45184800-45189000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:45185000-45187200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:45185000-45187400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr1:45185000-45187600	Enhancers	Primary B cells from cord blood	blood
36	chr1:45185200-45187400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr1:45185200-45187600	Weak transcription	Osteobl	bone
38	chr1:45185200-45189200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:45185200-45190600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:45185200-45192400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:45185400-45187400	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr1:45185400-45187800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:45185600-45187200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:45185600-45187400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:45185600-45192200	Weak transcription	NHDF-Ad	bronchial
46	chr1:45185600-45194800	Weak transcription	Dnd41	blood
47	chr1:45185800-45189000	Enhancers	Primary B cells from peripheral blood	blood
48	chr1:45186000-45186200	Enhancers	HSMM	muscle
49	chr1:45186000-45188000	Enhancers	HepG2	liver
50	chr1:45186000-45188800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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