Variant report

Variant	rs2864700
Chromosome Location	chr1:151028929-151028930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151027735-151029650	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:151019747-151029675	K562	blood:	n/a	n/a
3	POLR2A	chr1:151023510-151029710	K562	blood:	n/a	n/a
4	POLR2A	chr1:151027298-151029427	K562	blood:	n/a	n/a
5	TBL1XR1	chr1:151028597-151029406	K562	blood:	n/a	n/a
6	POLR2A	chr1:151027701-151029673	GM12892	blood:	n/a	n/a
7	GATA3	chr1:151028531-151029549	MCF-7	breast:	n/a	chr1:151028903-151028914
8	MAX	chr1:151028826-151029672	MCF-7	breast:	n/a	n/a
9	MYC	chr1:151028681-151029473	K562	blood:	n/a	chr1:151028701-151028711
10	POLR2A	chr1:151027353-151029436	K562	blood:	n/a	n/a
11	MYC	chr1:151028519-151029539	K562	blood:	n/a	chr1:151028701-151028711
12	MXI1	chr1:151028740-151029414	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:151021903-151029745	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:151028886-151028997	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:151027220-151029690	K562	blood:	n/a	n/a
16	TEAD4	chr1:151028193-151029461	K562	blood:	n/a	n/a
17	POLR2A	chr1:151028399-151029645	K562	blood:	n/a	n/a
18	STAT1	chr1:151028885-151028994	GM12878	blood:	n/a	n/a
19	RUNX3	chr1:151028634-151029030	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:151028691-151028984	IMR90	lung:	n/a	n/a
21	POLR2A	chr1:151028571-151029733	K562	blood:	n/a	n/a
22	FOXA1	chr1:151028924-151029325	T-47D	breast:	n/a	n/a
23	POLR2A	chr1:151028371-151029658	GM12892	blood:	n/a	n/a
24	GATA3	chr1:151028917-151029367	T-47D	breast:	n/a	n/a
25	POLR2A	chr1:151028179-151029534	GM12878	blood:	n/a	n/a
26	TBL1XR1	chr1:151028900-151029202	K562	blood:	n/a	n/a
27	POLR2A	chr1:151028548-151029567	GM12892	blood:	n/a	n/a
28	POLR2A	chr1:151027457-151029400	K562	blood:	n/a	n/a
29	MAZ	chr1:151028620-151028935	GM12878	blood:	n/a	chr1:151028701-151028711
30	POLR2A	chr1:151027138-151029730	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151005028..151012583-chr1:151026392..151034442,13	K562	blood:
2	chr1:150549378..150552816-chr1:151028901..151032004,3	K562	blood:
3	chr1:150950574..150954547-chr1:151027400..151032185,6	MCF-7	breast:
4	chr1:150980774..150986118-chr1:151028117..151032528,6	MCF-7	breast:
5	chr1:151027658..151029409-chr1:151300296..151301858,2	K562	blood:
6	chr1:150976723..150987587-chr1:151024685..151036322,24	MCF-7	breast:
7	chr1:151027474..151029846-chr1:151254006..151256082,2	MCF-7	breast:

No data

Variant related genes	Relation type
MLLT11	TF binding region
ENSG00000143373	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000273481	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143412	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10788797	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs15740	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs2091219	0.82[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2902810	0.89[JPT][hapmap]
rs3738476	0.84[ASN][1000 genomes]
rs4357530	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs4589116	0.84[ASN][1000 genomes]
rs4970941	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs4970989	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4970991	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs6587552	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6587553	0.89[JPT][hapmap]
rs6656450	1.00[CHB][hapmap]
rs6676190	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs6691701	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs6694158	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2864700	CDC42SE1	cis	multi-tissue	Pritchard
rs2864700	GABPB2	cis	cerebellum	SCAN
rs2864700	CDC42SE1	cis	parietal	SCAN
rs2864700	LYSMD1	cis	parietal	SCAN
rs2864700	GOLPH3L	cis	frontal cortex	BrainEAC
rs2864700	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs2864700	CDC42SE1	cis	lymphoblastoid	seeQTL
rs2864700	SEMA6C	cis	parietal	SCAN
rs2864700	BNIPL	cis	lung	GTEx
rs2864700	LYSMD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151021200-151030400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:151021400-151029000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:151021400-151030000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:151022000-151030000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:151022400-151029000	Strong transcription	NH-A	brain
6	chr1:151022400-151029200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr1:151022400-151029200	Strong transcription	NHDF-Ad	bronchial
8	chr1:151022400-151029400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:151022600-151029200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:151022800-151029400	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:151022800-151029600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:151022800-151029600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:151023200-151029600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:151023400-151029200	Strong transcription	Fetal Brain Female	brain
15	chr1:151023800-151029000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:151024000-151029000	Strong transcription	Fetal Lung	lung
17	chr1:151024200-151029200	Strong transcription	Brain Angular Gyrus	brain
18	chr1:151024200-151029400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:151024200-151030000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:151024200-151030200	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr1:151024400-151029000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:151024400-151029200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:151024400-151029400	Strong transcription	Aorta	Aorta
24	chr1:151026000-151029200	Genic enhancers	Esophagus	oesophagus
25	chr1:151026200-151031000	Weak transcription	Ovary	ovary
26	chr1:151026600-151029200	Strong transcription	Fetal Kidney	kidney
27	chr1:151026600-151029800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:151026800-151030800	Transcr. at gene 5' and 3'	K562	blood
29	chr1:151027000-151029200	Genic enhancers	HMEC	breast
30	chr1:151027200-151029200	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
31	chr1:151027200-151029200	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
32	chr1:151027200-151029400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
33	chr1:151027200-151029800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
34	chr1:151027200-151032000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
35	chr1:151027400-151029600	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
36	chr1:151027400-151030000	Genic enhancers	Placenta	Placenta
37	chr1:151027400-151030200	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
38	chr1:151027600-151029400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:151027600-151029400	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:151027600-151030400	Genic enhancers	Fetal Intestine Small	intestine
41	chr1:151027600-151030400	Genic enhancers	HepG2	liver
42	chr1:151027800-151029000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:151027800-151029200	Weak transcription	Fetal Brain Male	brain
44	chr1:151027800-151029400	Genic enhancers	Adipose Nuclei	Adipose
45	chr1:151027800-151029400	Genic enhancers	Liver	Liver
46	chr1:151027800-151029600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:151027800-151029600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
48	chr1:151027800-151029800	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:151027800-151029800	Genic enhancers	Right Ventricle	heart
50	chr1:151027800-151030000	Genic enhancers	Colon Smooth Muscle	Colon

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