Variant report

Variant	rs3795702
Chromosome Location	chr1:150545624-150545625
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	POLR2A	chr1:150545239-150545969	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:150545530-150545729	A549	lung:	n/a	n/a
3	PAX5	chr1:150545460-150546134	GM12878	blood:	n/a	chr1:150545489-150545498 chr1:150545486-150545495
4	POLR2A	chr1:150545420-150546566	GM12891	blood:	n/a	n/a
5	NFYB	chr1:150545559-150545987	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:150543194-150546558	HepG2	liver:	n/a	n/a
7	MTA3	chr1:150544950-150546278	GM12878	blood:	n/a	n/a
8	CHD2	chr1:150545566-150545914	Hela-S3	cervix:	n/a	n/a
9	CREB1	chr1:150545416-150546280	K562	blood:	n/a	n/a
10	POLR2A	chr1:150545493-150545770	HepG2	liver:	n/a	n/a
11	ATF2	chr1:150545129-150546556	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr1:150545338-150545716	GM12878	blood:	n/a	n/a
13	ZNF143	chr1:150545348-150545878	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:150538698-150546656	H1-hESC	embryonic stem cell:	n/a	n/a
15	WRNIP1	chr1:150545536-150545922	GM12878	blood:	n/a	n/a
16	CCNT2	chr1:150545457-150546315	K562	blood:	n/a	n/a
17	POLR2A	chr1:150544288-150546564	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:150538889-150552727	K562	blood:	n/a	n/a
19	POLR2A	chr1:150538866-150546573	U87	brain:	n/a	n/a
20	POLR2A	chr1:150539774-150546448	HUVEC	blood vessel:	n/a	n/a
21	CHD2	chr1:150544925-150546197	K562	blood:	n/a	n/a
22	POLR2A	chr1:150545612-150545966	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr1:150541963-150546408	HUVEC	blood vessel:	n/a	n/a
24	TEAD4	chr1:150544936-150546577	K562	blood:	n/a	n/a
25	NFATC1	chr1:150545293-150546213	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:150543224-150546653	K562	blood:	n/a	n/a
27	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
28	SIN3AK20	chr1:150543601-150546543	K562	blood:	n/a	n/a
29	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
30	POU2F2	chr1:150545494-150546201	GM12891	blood:	n/a	chr1:150545873-150545885 chr1:150545875-150545886 chr1:150545873-150545886 chr1:150545874-150545884 chr1:150545872-150545887 chr1:150545875-150545885 chr1:150545876-150545884 chr1:150545871-150545889 chr1:150545874-150545884
31	POU2F2	chr1:150545398-150546416	GM12891	blood:	n/a	chr1:150545873-150545885 chr1:150545875-150545886 chr1:150545873-150545886 chr1:150545874-150545884 chr1:150545872-150545887 chr1:150545875-150545885 chr1:150545876-150545884 chr1:150545871-150545889 chr1:150545874-150545884
32	YY1	chr1:150545572-150545725	K562	blood:	n/a	n/a
33	POLR2A	chr1:150540216-150546538	U87	brain:	n/a	n/a
34	NFYA	chr1:150545547-150546013	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr1:150544471-150546444	GM12892	blood:	n/a	n/a
36	POLR2A	chr1:150545405-150546201	HepG2	liver:	n/a	n/a
37	POLR2A	chr1:150538654-150552953	Hela-S3	cervix:	n/a	n/a
38	EGR1	chr1:150545493-150546190	K562	blood:	n/a	n/a
39	USF2	chr1:150545621-150546053	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr1:150544818-150546306	HUVEC	blood vessel:	n/a	n/a
41	SPI1	chr1:150545110-150546000	GM12878	blood:	n/a	chr1:150545489-150545498 chr1:150545485-150545494
42	POLR2A	chr1:150543314-150546680	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr1:150539727-150546572	HepG2	liver:	n/a	n/a
44	ZZZ3	chr1:150545376-150545902	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr1:150545436-150546521	HL-60	blood:	n/a	n/a
46	SPI1	chr1:150545276-150545706	GM12878	blood:	n/a	chr1:150545489-150545498 chr1:150545485-150545494
47	USF2	chr1:150545607-150546027	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:150530539-150552850	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr1:150538736-150552926	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:150538866-150553173	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150258806..150260952-chr1:150544503..150546807,2	K562	blood:
2	chr1:150455770..150459652-chr1:150544183..150547234,4	K562	blood:
3	chr1:150543953..150547860-chr1:150600449..150605575,7	K562	blood:
4	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
5	chr1:150543938..150548482-chr1:150576509..150579510,5	K562	blood:
6	chr1:150543642..150545689-chr1:150586263..150588774,2	MCF-7	breast:
7	chr1:150545565..150549511-chr1:150783335..150787451,6	K562	blood:
8	chr1:150544693..150547632-chr1:150583989..150587707,3	MCF-7	breast:
9	chr1:150544010..150546916-chr1:150590925..150592477,2	MCF-7	breast:
10	chr1:150543916..150546115-chr1:150744599..150746718,2	K562	blood:
11	chr1:150542528..150547161-chr1:150576124..150579510,4	K562	blood:
12	chr1:150545107..150547028-chr1:150615492..150618208,2	K562	blood:
13	chr1:150545388..150547945-chr1:150570621..150572716,2	K562	blood:
14	chr1:150455770..150457599-chr1:150544025..150546783,3	K562	blood:
15	chr1:150545217..150545899-chr13:115045990..115046741,2	Hela-S3	cervix:
16	chr1:150545422..150545983-chrX:24043803..24044458,2	Hela-S3	cervix:
17	chr1:150542997..150546031-chr1:150978720..150981188,4	MCF-7	breast:
18	chr1:150545363..150545970-chr1:153643040..153643654,2	Hela-S3	cervix:
19	chr1:150545613..150547144-chr1:150678229..150680325,2	K562	blood:
20	chr1:150435919..150438376-chr1:150544338..150547064,3	K562	blood:
21	chr1:150545560..150548928-chr1:150668482..150671179,4	K562	blood:
22	chr1:150545274..150547768-chr1:150592688..150595152,4	MCF-7	breast:

Variant related genes	Relation type
RN7SL600P	TF binding region
ENSG00000143409	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000143452	Chromatin interaction
ENSG00000143457	Chromatin interaction
ENSG00000143420	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11204667	1.00[ASN][1000 genomes]
rs11810419	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12097596	1.00[JPT][hapmap]
rs16836594	0.86[CHB][hapmap]
rs16836601	0.86[CHB][hapmap]
rs16836786	0.86[CHB][hapmap]
rs16836943	0.86[CHB][hapmap]
rs2275245	0.86[CHB][hapmap]
rs3806389	0.86[CHB][hapmap];1.00[AFR][1000 genomes]
rs3850843	0.86[CHB][hapmap]
rs4970925	0.86[CHB][hapmap];1.00[AFR][1000 genomes]
rs4970927	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs4970947	1.00[AFR][1000 genomes]
rs4971044	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs55975034	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57263353	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs58537074	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58550476	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58585637	1.00[AFR][1000 genomes]
rs6663989	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs871527	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150534400-150547200	Weak transcription	Ovary	ovary
2	chr1:150541400-150545800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:150541400-150547200	Genic enhancers	Fetal Intestine Small	intestine
4	chr1:150541400-150549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:150541800-150546800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:150542000-150547200	Genic enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:150542200-150547200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:150542200-150547200	Strong transcription	Brain Germinal Matrix	brain
9	chr1:150542200-150548000	Genic enhancers	Placenta	Placenta
10	chr1:150542400-150546800	Genic enhancers	Fetal Muscle Leg	muscle
11	chr1:150542400-150547000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:150542600-150547200	Genic enhancers	Lung	lung
13	chr1:150542600-150548200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:150542800-150545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:150542800-150547800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:150542800-150551600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
17	chr1:150543000-150546000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:150543000-150549200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:150543200-150545800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:150543200-150547000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:150543400-150547000	Genic enhancers	Osteobl	bone
22	chr1:150543600-150547200	Genic enhancers	Dnd41	blood
23	chr1:150543600-150547800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:150543600-150548200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
27	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:150543800-150547000	Strong transcription	Fetal Lung	lung
29	chr1:150544000-150545800	Strong transcription	Thymus	Thymus
30	chr1:150544000-150547000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:150544000-150547200	Strong transcription	Fetal Stomach	stomach
32	chr1:150544000-150547400	Weak transcription	Fetal Brain Male	brain
33	chr1:150544200-150551600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
34	chr1:150544400-150546000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:150544400-150546400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:150544400-150547200	Genic enhancers	Fetal Intestine Large	intestine
37	chr1:150544600-150551600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
38	chr1:150544800-150545800	Genic enhancers	Psoas Muscle	Psoas
39	chr1:150544800-150546800	Genic enhancers	HUVEC	blood vessel
40	chr1:150544800-150547000	Genic enhancers	Left Ventricle	heart
41	chr1:150544800-150548400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:150545000-150546200	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
43	chr1:150545000-150546200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
44	chr1:150545000-150546600	Genic enhancers	Colonic Mucosa	Colon
45	chr1:150545000-150546800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:150545000-150546800	Genic enhancers	HMEC	breast
47	chr1:150545000-150547200	Genic enhancers	A549	lung
48	chr1:150545000-150548600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:150545000-150550000	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
50	chr1:150545000-150551400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood

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