Variant report

Variant	rs6490287
Chromosome Location	chr12:120637474-120637475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:97)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:97 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120631371-120639781	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr12:120636178-120639074	A549	lung:	n/a	n/a
3	POLR2A	chr12:120636252-120638005	GM12878	blood:	n/a	n/a
4	MXI1	chr12:120636976-120637908	K562	blood:	n/a	n/a
5	BACH1	chr12:120637435-120637866	K562	blood:	n/a	n/a
6	POLR2A	chr12:120632029-120639863	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:120636195-120639774	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:120636720-120638123	K562	blood:	n/a	n/a
9	POLR2A	chr12:120636127-120639423	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr12:120636151-120638027	GM12891	blood:	n/a	n/a
11	POLR2A	chr12:120636471-120639372	HL-60	blood:	n/a	n/a
12	MXI1	chr12:120637248-120639868	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr12:120635673-120639688	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:120632203-120639596	K562	blood:	n/a	n/a
15	POLR2A	chr12:120636703-120637980	HepG2	liver:	n/a	n/a
16	POLR2A	chr12:120636707-120637517	HCT-116	colon:	n/a	n/a
17	POLR2A	chr12:120636111-120637525	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:120636420-120639604	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr12:120635716-120639431	GM12892	blood:	n/a	n/a
20	POLR2A	chr12:120631475-120639779	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:120632190-120639605	GM12892	blood:	n/a	n/a
22	POLR2A	chr12:120636042-120639720	PANC-1	pancreas:	n/a	n/a
23	HCFC1	chr12:120637009-120639736	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr12:120632031-120639569	GM12892	blood:	n/a	n/a
25	POLR2A	chr12:120636133-120639305	U87	brain:	n/a	n/a
26	HEY1	chr12:120636156-120637525	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:120635672-120639608	GM12891	blood:	n/a	n/a
28	TAL1	chr12:120637232-120639288	K562	blood:	n/a	n/a
29	POLR2A	chr12:120636745-120637487	HepG2	liver:	n/a	n/a
30	WRNIP1	chr12:120637117-120637960	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:120636479-120637527	HL-60	blood:	n/a	n/a
32	TAF7	chr12:120637089-120637888	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr12:120637375-120637526	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr12:120637385-120639612	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr12:120636010-120639485	HUVEC	blood vessel:	n/a	n/a
36	BRCA1	chr12:120637362-120637737	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr12:120635799-120639930	HepG2	liver:	n/a	n/a
38	MAFF	chr12:120637360-120637990	K562	blood:	n/a	chr12:120637814-120637832
39	POLR2A	chr12:120636372-120639631	GM18505	blood:	n/a	n/a
40	POLR2A	chr12:120635694-120639558	GM12891	blood:	n/a	n/a
41	POLR2A	chr12:120632184-120639485	GM12891	blood:	n/a	n/a
42	POLR2A	chr12:120636567-120639601	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr12:120636039-120639896	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr12:120636203-120637529	GM12878	blood:	n/a	n/a
45	NFYB	chr12:120637299-120637542	GM12878	blood:	n/a	chr12:120637451-120637461 chr12:120637450-120637463
46	POLR2A	chr12:120631828-120639777	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr12:120632144-120640040	Hela-S3	cervix:	n/a	n/a
48	PML	chr12:120637105-120639734	GM12878	blood:	n/a	n/a
49	CHD1	chr12:120637004-120639322	H1-hESC	embryonic stem cell:	n/a	n/a
50	MTA3	chr12:120636700-120639440	GM12878	blood:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120628864..120642103-chr12:120725347..120732286,54	K562	blood:
2	chr12:120628211..120641965-chr12:120660551..120674110,39	K562	blood:
3	chr12:120637393..120639950-chr3:39193278..39195443,2	K562	blood:
4	chr12:120551826..120556882-chr12:120630846..120640383,26	K562	blood:
5	chr12:120634142..120641127-chr12:120698850..120705439,14	K562	blood:
6	chr12:120576167..120578821-chr12:120637302..120640400,3	K562	blood:
7	chr12:120626707..120642605-chr12:120719450..120732919,96	MCF-7	breast:
8	chr12:120637307..120638899-chr6:27776878..27779705,2	K562	blood:
9	chr12:120591212..120593499-chr12:120637198..120638794,2	MCF-7	breast:
10	chr12:120637319..120639058-chr12:120965439..120967173,2	K562	blood:
11	chr12:120552903..120558662-chr12:120635855..120639972,12	MCF-7	breast:
12	chr12:120554994..120557100-chr12:120637245..120639085,2	MCF-7	breast:
13	chr12:120574814..120578175-chr12:120636472..120639249,3	MCF-7	breast:
14	chr12:120636290..120639093-chr17:59486664..59489640,2	MCF-7	breast:
15	chr12:120553041..120557313-chr12:120636619..120640383,10	K562	blood:
16	chr12:120637319..120640372-chr12:120965439..120969225,4	K562	blood:
17	chr12:120637262..120638804-chr19:58898635..58900812,2	MCF-7	breast:
18	chr12:120636466..120640337-chr12:120966729..120969535,3	MCF-7	breast:
19	chr12:120637343..120639223-chr17:56707598..56709431,2	MCF-7	breast:
20	chr12:120631139..120640506-chr12:120724902..120734482,54	K562	blood:
21	chr12:120636494..120638550-chr12:120756430..120759190,2	MCF-7	breast:
22	chr12:120635810..120640156-chr12:120882395..120885946,4	K562	blood:
23	chr12:120636894..120638425-chr19:51313714..51316049,2	K562	blood:

No data

Variant related genes	Relation type
PXN-AS1	TF binding region
GCN1L1	TF binding region
RPLP0	TF binding region
ENSG00000266704	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000257218	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000110871	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000170855	Chromatin interaction
ENSG00000144655	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000083845	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000089154	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10735071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10774543	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230540	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12308065	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286046	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2696029	1.00[JPT][hapmap]
rs3845191	1.00[ASN][1000 genomes]
rs3956837	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766959	0.92[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767884	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6490286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7298516	1.00[JPT][hapmap]
rs7960843	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7968689	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978656	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs965791	1.00[JPT][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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6490287	DYNLL1	cis	parietal	SCAN
rs6490287	GCN1L1	cis	parietal	SCAN
rs6490287	NME2P1	cis	parietal	SCAN
rs6490287	CCDC64	cis	parietal	SCAN
rs6490287	GCN1L1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120633000-120637800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:120633200-120638400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:120633400-120637600	Genic enhancers	Liver	Liver
4	chr12:120633600-120638000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
5	chr12:120633600-120638200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:120633800-120637600	Genic enhancers	Placenta	Placenta
7	chr12:120633800-120638600	Transcr. at gene 5' and 3'	K562	blood
8	chr12:120634000-120637600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:120634400-120637800	Transcr. at gene 5' and 3'	Hela-S3	cervix
10	chr12:120634600-120637600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:120634800-120637600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:120634800-120637600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:120634800-120638600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
14	chr12:120634800-120638600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
15	chr12:120634800-120638800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
16	chr12:120635000-120637600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:120635000-120637800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr12:120635000-120638400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:120635000-120638800	Transcr. at gene 5' and 3'	A549	lung
20	chr12:120635200-120637800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:120635400-120638000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
22	chr12:120635400-120638200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
23	chr12:120635800-120637600	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr12:120635800-120638800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
25	chr12:120635800-120639000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:120636000-120637800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
27	chr12:120636200-120637600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr12:120636200-120637800	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr12:120636200-120637800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:120636200-120637800	Transcr. at gene 5' and 3'	HUVEC	blood vessel
31	chr12:120636200-120637800	Transcr. at gene 5' and 3'	Osteobl	bone
32	chr12:120636200-120638000	Transcr. at gene 5' and 3'	HMEC	breast
33	chr12:120636200-120638000	Transcr. at gene 5' and 3'	NHEK	skin
34	chr12:120636200-120638200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:120636200-120638800	Transcr. at gene 5' and 3'	Dnd41	blood
36	chr12:120636400-120637600	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr12:120636400-120637800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:120636400-120637800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:120636400-120637800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:120636400-120637800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:120636400-120637800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
42	chr12:120636400-120638000	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
43	chr12:120636400-120638000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
44	chr12:120636400-120638000	Transcr. at gene 5' and 3'	HepG2	liver
45	chr12:120636400-120638000	Transcr. at gene 5' and 3'	NH-A	brain
46	chr12:120636400-120638200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:120636400-120638200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
48	chr12:120636600-120637600	Genic enhancers	Colonic Mucosa	Colon
49	chr12:120636600-120638000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
50	chr12:120636600-120638000	Transcr. at gene 5' and 3'	HSMM	muscle

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