Variant report

Variant	rs2901092
Chromosome Location	chr1:169456393-169456394
allele	A/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	MXI1	chr1:169453845-169456810	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:169452374-169456758	MCF10A-Er-Src	breast:	n/a	n/a
3	SMARCC2	chr1:169454355-169456428	Hela-S3	cervix:	n/a	n/a
4	KAP1	chr1:169455068-169457749	HEK293	kidney:	n/a	chr1:169456899-169456907 chr1:169456870-169456878
5	POLR2A	chr1:169453946-169456497	H1-hESC	embryonic stem cell:	n/a	n/a
6	RFX5	chr1:169454125-169456976	SK-N-SH	brain:	n/a	chr1:169455259-169455268
7	MYC	chr1:169454124-169456520	K562	blood:	n/a	n/a
8	GTF2F1	chr1:169454974-169456486	Hela-S3	cervix:	n/a	n/a
9	SMARCC1	chr1:169454279-169456519	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:169452526-169456603	MCF10A-Er-Src	breast:	n/a	n/a
11	TAL1	chr1:169454908-169456457	K562	blood:	n/a	n/a
12	KAP1	chr1:169455192-169456918	U2OS	brain:	n/a	chr1:169456899-169456907 chr1:169456870-169456878
13	POLR2A	chr1:169451926-169456727	IMR90	lung:	n/a	n/a
14	HCFC1	chr1:169452490-169456441	Hela-S3	cervix:	n/a	n/a
15	CHD1	chr1:169452645-169456936	IMR90	lung:	n/a	chr1:169453020-169453027 chr1:169455009-169455019 chr1:169454476-169454486
16	MYC	chr1:169454386-169456393	A549	lung:	n/a	n/a
17	JUND	chr1:169456367-169456751	HepG2	liver:	n/a	n/a
18	JUND	chr1:169454438-169456748	K562	blood:	n/a	chr1:169455928-169455939
19	CTCF	chr1:169456300-169456450	HBMEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:169453983-169456483	HepG2	liver:	n/a	n/a
21	MXI1	chr1:169452580-169456608	IMR90	lung:	n/a	n/a
22	RFX5	chr1:169454376-169456543	Hela-S3	cervix:	n/a	chr1:169455259-169455268
23	JUN	chr1:169456385-169456691	K562	blood:	n/a	chr1:169456556-169456569
24	JUN	chr1:169456373-169456728	HepG2	liver:	n/a	chr1:169456556-169456569

No.	Distal block	Cell Line	Cell type
1	chr1:169451858..169456935-chr1:169476541..169486862,15	MCF-7	breast:
2	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
3	chr1:169454326..169457851-chr1:169761976..169765744,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BLZF1-2	chr1:169455353-169458414	NONHSAT007465
2	lnc-BLZF1-2	chr1:169455380-169456846	NONHSAT139913

Variant related genes	Relation type
SLC19A2	TF binding region
ENSG00000000460	Chromatin interaction
ENSG00000171806	Chromatin interaction
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10800430	1.00[YRI][hapmap]
rs10919151	0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10919156	1.00[YRI][hapmap]
rs10919157	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10919159	1.00[YRI][hapmap]
rs11810815	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs12059944	0.80[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12071630	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12073439	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs12074966	0.81[ASN][1000 genomes]
rs12081030	1.00[YRI][hapmap]
rs12091133	0.84[AFR][1000 genomes]
rs12091844	0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs12092952	0.84[AFR][1000 genomes]
rs12097682	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2038024	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2072757	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2275300	1.00[YRI][hapmap]
rs2280257	1.00[YRI][hapmap]
rs3737683	0.81[ASN][1000 genomes]
rs3765227	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3766088	0.82[ASW][hapmap]
rs9628661	1.00[YRI][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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169448000-169457000	Active TSS	Right Ventricle	heart
2	chr1:169451600-169457000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:169452600-169457000	Active TSS	Left Ventricle	heart
4	chr1:169453400-169456600	Active TSS	Aorta	Aorta
5	chr1:169453600-169457000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:169453600-169457200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:169453800-169456400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr1:169453800-169456400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:169454200-169456400	Active TSS	Thymus	Thymus
10	chr1:169454400-169456600	Active TSS	Brain Cingulate Gyrus	brain
11	chr1:169454400-169458400	Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr1:169454600-169456400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:169455400-169456400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr1:169455400-169456400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr1:169455400-169456400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr1:169455400-169456400	Flanking Active TSS	HUVEC	blood vessel
17	chr1:169455400-169456600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:169455600-169456400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr1:169455600-169456400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:169455600-169456400	Active TSS	Right Atrium	heart
21	chr1:169455600-169456400	Flanking Active TSS	HMEC	breast
22	chr1:169455600-169456400	Flanking Active TSS	NHEK	skin
23	chr1:169455600-169456600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr1:169455600-169456600	Flanking Active TSS	NH-A	brain
25	chr1:169455600-169457000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr1:169455600-169457400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr1:169455800-169456400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:169455800-169456400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr1:169455800-169456400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:169455800-169456400	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr1:169455800-169456400	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr1:169455800-169456400	Flanking Active TSS	Fetal Brain Female	brain
33	chr1:169455800-169456400	Flanking Active TSS	Fetal Kidney	kidney
34	chr1:169455800-169456400	Flanking Active TSS	Fetal Lung	lung
35	chr1:169455800-169456400	Flanking Active TSS	A549	lung
36	chr1:169455800-169456400	Flanking Active TSS	GM12878-XiMat	blood
37	chr1:169455800-169456600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:169455800-169456600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr1:169455800-169456800	Flanking Active TSS	Fetal Heart	heart
40	chr1:169455800-169456800	Flanking Active TSS	Fetal Stomach	stomach
41	chr1:169455800-169456800	Flanking Active TSS	Hela-S3	cervix
42	chr1:169455800-169456800	Flanking Active TSS	HSMM	muscle
43	chr1:169455800-169457000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:169455800-169457200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:169455800-169457200	Flanking Active TSS	HSMMtube	muscle
46	chr1:169455800-169457600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:169455800-169457800	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr1:169455800-169461400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:169456000-169456400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:169456000-169456400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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