Variant report

Variant	rs2038024
Chromosome Location	chr1:169455982-169455983
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:101)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:101 , 50 per page) page: 1 2 3

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	BRCA1	chr1:169454999-169456158	Hela-S3	cervix:	n/a	n/a
3	MAX	chr1:169453879-169456142	Hela-S3	cervix:	n/a	n/a
4	MYC	chr1:169454014-169456207	MCF10A-Er-Src	breast:	n/a	n/a
5	SIX5	chr1:169455243-169456008	A549	lung:	n/a	n/a
6	POLR2A	chr1:169454437-169455995	K562	blood:	n/a	n/a
7	FOS	chr1:169455187-169456214	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:169452374-169456758	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:169454348-169456091	K562	blood:	n/a	n/a
10	CHD2	chr1:169454309-169456107	Hela-S3	cervix:	n/a	chr1:169455009-169455019 chr1:169454476-169454486
11	CEBPB	chr1:169452668-169456351	Hela-S3	cervix:	n/a	n/a
12	ZKSCAN1	chr1:169454959-169456204	Hela-S3	cervix:	n/a	n/a
13	MAZ	chr1:169454306-169456157	Hela-S3	cervix:	n/a	n/a
14	SMC3	chr1:169454134-169456361	Hela-S3	cervix:	n/a	n/a
15	MYC	chr1:169454386-169455985	K562	blood:	n/a	n/a
16	SMARCC2	chr1:169454355-169456428	Hela-S3	cervix:	n/a	n/a
17	KAP1	chr1:169455068-169457749	HEK293	kidney:	n/a	chr1:169456899-169456907 chr1:169456870-169456878
18	MAX	chr1:169454359-169456170	Hela-S3	cervix:	n/a	n/a
19	EP300	chr1:169455010-169456270	K562	blood:	n/a	n/a
20	TCF7L2	chr1:169454497-169456040	Hela-S3	cervix:	n/a	n/a
21	JUND	chr1:169455874-169456053	HepG2	liver:	n/a	chr1:169455928-169455939
22	MAX	chr1:169455880-169456030	H1-hESC	embryonic stem cell:	n/a	n/a
23	E2F6	chr1:169454340-169456043	K562	blood:	n/a	chr1:169454770-169454782 chr1:169454768-169454783
24	POLR2A	chr1:169453914-169456288	K562	blood:	n/a	n/a
25	BACH1	chr1:169455042-169456077	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:169454806-169456128	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr1:169454030-169456069	PBDE	blood:	n/a	n/a
28	ELK1	chr1:169454899-169456020	Hela-S3	cervix:	n/a	n/a
29	SIN3AK20	chr1:169452581-169456049	MCF-7	breast:	n/a	n/a
30	NR2F2	chr1:169454303-169456163	K562	blood:	n/a	n/a
31	FOS	chr1:169455212-169456264	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr1:169454272-169456290	HepG2	liver:	n/a	n/a
33	ZC3H11A	chr1:169455129-169456113	K562	blood:	n/a	n/a
34	STAT3	chr1:169455444-169456326	Hela-S3	cervix:	n/a	n/a
35	EP300	chr1:169454979-169456069	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:169454050-169456241	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:169453946-169456497	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr1:169454936-169456034	GM12891	blood:	n/a	n/a
39	RFX5	chr1:169454125-169456976	SK-N-SH	brain:	n/a	chr1:169455259-169455268
40	POLR2A	chr1:169454345-169456175	GM12878	blood:	n/a	n/a
41	ZNF143	chr1:169455020-169455994	K562	blood:	n/a	n/a
42	CEBPB	chr1:169455342-169456193	IMR90	lung:	n/a	n/a
43	RAD21	chr1:169455002-169456088	Hela-S3	cervix:	n/a	n/a
44	STAT3	chr1:169455826-169456026	MCF10A-Er-Src	breast:	n/a	n/a
45	MYC	chr1:169454343-169456228	K562	blood:	n/a	n/a
46	STAT3	chr1:169455670-169456120	MCF10A-Er-Src	breast:	n/a	n/a
47	MYC	chr1:169454124-169456520	K562	blood:	n/a	n/a
48	MYC	chr1:169455008-169456266	MCF10A-Er-Src	breast:	n/a	n/a
49	MYC	chr1:169454347-169456062	Hela-S3	cervix:	n/a	n/a
50	GTF2F1	chr1:169454974-169456486	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

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:

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

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

No data

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

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10919151	0.88[JPT][hapmap]
rs11810815	0.84[JPT][hapmap]
rs12059944	0.80[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs12074966	0.81[ASN][1000 genomes]
rs12091844	0.81[ASN][1000 genomes]
rs2072757	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2901092	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3737683	0.81[ASN][1000 genomes]
rs3765227	0.81[ASN][1000 genomes]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2038024	ADCY10	cis	cerebellum	SCAN
rs2038024	XCL2	cis	cerebellum	SCAN

Chromatin state (count:123 , 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	chr1:169450000-169456000	Active TSS	Psoas Muscle	Psoas
3	chr1:169451600-169457000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:169452200-169456200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:169452600-169457000	Active TSS	Left Ventricle	heart
6	chr1:169452800-169456000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:169452800-169456000	Active TSS	Stomach Smooth Muscle	stomach
8	chr1:169452800-169456200	Active TSS	Ovary	ovary
9	chr1:169453200-169456000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr1:169453200-169456000	Active TSS	Placenta	Placenta
11	chr1:169453200-169456200	Active TSS	Pancreas	Pancrea
12	chr1:169453400-169456000	Active TSS	Colonic Mucosa	Colon
13	chr1:169453400-169456200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:169453400-169456600	Active TSS	Aorta	Aorta
15	chr1:169453600-169456000	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr1:169453600-169456200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:169453600-169457000	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr1:169453600-169457200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:169453800-169456000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:169453800-169456200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:169453800-169456400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:169453800-169456400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:169454000-169456200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr1:169454000-169456200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:169454000-169456200	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr1:169454200-169456000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:169454200-169456200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr1:169454200-169456400	Active TSS	Thymus	Thymus
29	chr1:169454400-169456000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:169454400-169456000	Active TSS	Liver	Liver
31	chr1:169454400-169456000	Active TSS	Brain Anterior Caudate	brain
32	chr1:169454400-169456000	Active TSS	Stomach Mucosa	stomach
33	chr1:169454400-169456200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:169454400-169456200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:169454400-169456200	Active TSS	Brain Substantia Nigra	brain
36	chr1:169454400-169456200	Active TSS	NHDF-Ad	bronchial
37	chr1:169454400-169456600	Active TSS	Brain Cingulate Gyrus	brain
38	chr1:169454400-169458400	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr1:169454600-169456000	Active TSS	Brain Angular Gyrus	brain
40	chr1:169454600-169456000	Active TSS	Placenta Amnion	Placenta Amnion
41	chr1:169454600-169456400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:169454800-169456000	Active TSS	Fetal Muscle Trunk	muscle
43	chr1:169455000-169456200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:169455400-169456000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr1:169455400-169456000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr1:169455400-169456200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr1:169455400-169456200	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr1:169455400-169456200	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr1:169455400-169456200	Flanking Active TSS	Dnd41	blood
50	chr1:169455400-169456200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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