Variant report

Variant	rs2241529
Chromosome Location	chr10:54074757-54074758
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	CTCF	chr10:54074660-54074810	HFF	foreskin:	n/a	n/a
2	MAFK	chr10:54074667-54074881	IMR90	lung:	n/a	n/a
3	MAX	chr10:54073032-54075312	A549	lung:	n/a	n/a
4	POLR2A	chr10:54072994-54075187	MCF-7	breast:	n/a	n/a
5	RAD21	chr10:54073842-54074887	IMR90	lung:	n/a	chr10:54074080-54074090 chr10:54074078-54074091
6	CTCF	chr10:54074655-54074823	MCF-7	breast:	n/a	n/a
7	CREB1	chr10:54073666-54074925	HepG2	liver:	n/a	n/a
8	POLR2A	chr10:54073615-54076920	HUVEC	blood vessel:	n/a	n/a
9	MAZ	chr10:54073295-54075277	IMR90	lung:	n/a	n/a
10	POLR2A	chr10:54073872-54075126	IMR90	lung:	n/a	n/a
11	MYC	chr10:54074600-54074859	MCF-7	breast:	n/a	n/a
12	PBX3	chr10:54073599-54074990	SK-N-SH	brain:	n/a	n/a
13	REST	chr10:54072922-54075349	A549	lung:	n/a	chr10:54073933-54073946
14	POLR2A	chr10:54073649-54074878	Hela-S3	cervix:	n/a	n/a
15	MYC	chr10:54074671-54074761	MCF-7	breast:	n/a	n/a
16	POLR2A	chr10:54072977-54075692	Gliobla	brain:	n/a	n/a
17	MYC	chr10:54074715-54074809	HUVEC	blood vessel:	n/a	n/a
18	SP1	chr10:54073169-54075305	A549	lung:	n/a	chr10:54074927-54074937 chr10:54074910-54074919 chr10:54074913-54074927 chr10:54074927-54074936 chr10:54074926-54074938 chr10:54074905-54074914 chr10:54074909-54074921 chr10:54074923-54074937 chr10:54074911-54074920 chr10:54074926-54074938 chr10:54074910-54074920 chr10:54074909-54074921
19	REST	chr10:54073522-54074886	A549	lung:	n/a	chr10:54073933-54073946
20	BACH1	chr10:54074116-54074783	H1-hESC	embryonic stem cell:	n/a	n/a
21	RFX5	chr10:54073572-54074820	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr10:54073653-54075058	MCF-7	breast:	n/a	n/a
23	POLR2A	chr10:54073685-54075047	A549	lung:	n/a	n/a
24	CEBPB	chr10:54073697-54074786	Hela-S3	cervix:	n/a	n/a
25	RCOR1	chr10:54073874-54074772	Hela-S3	cervix:	n/a	n/a
26	PML	chr10:54073784-54075012	MCF-7	breast:	n/a	n/a
27	JUND	chr10:54073611-54075480	A549	lung:	n/a	n/a
28	POLR2A	chr10:54073464-54075557	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr10:54073903-54074872	IMR90	lung:	n/a	chr10:54073933-54073946
30	GATA2	chr10:54072878-54074785	SH-SY5Y	brain:	n/a	n/a
31	CTCF	chr10:54074667-54074813	MCF-7	breast:	n/a	n/a
32	SIN3AK20	chr10:54073685-54074907	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr10:54073525-54079363	HUVEC	blood vessel:	n/a	n/a
34	SIN3AK20	chr10:54073714-54074878	PANC-1	pancreas:	n/a	n/a
35	GATA2	chr10:54072971-54074768	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr10:54073092-54080655	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr10:54073389-54074853	HEK293	kidney:	n/a	n/a
38	CTCF	chr10:54072615-54075091	A549	lung:	n/a	chr10:54073933-54073946
39	POLR2A	chr10:54073646-54075420	MCF10A-Er-Src	breast:	n/a	n/a
40	GATA3	chr10:54073034-54075851	A549	lung:	n/a	chr10:54075334-54075351 chr10:54075069-54075076 chr10:54075068-54075078
41	RAD21	chr10:54073693-54074792	HCT-116	colon:	n/a	chr10:54074080-54074090 chr10:54074078-54074091
42	ZKSCAN1	chr10:54073909-54074841	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr10:54073880-54074886	HepG2	liver:	n/a	n/a
44	CTCF	chr10:54074660-54074810	AG04449	skin:	n/a	n/a
45	HEY1	chr10:54073574-54076765	HepG2	liver:	n/a	n/a
46	GATA3	chr10:54072834-54077297	SK-N-SH	brain:	n/a	chr10:54076036-54076046 chr10:54075334-54075351 chr10:54075069-54075076 chr10:54075068-54075078
47	BCL3	chr10:54072807-54075220	A549	lung:	n/a	chr10:54074906-54074919 chr10:54074911-54074920
48	MAX	chr10:54073616-54075200	SK-N-SH	brain:	n/a	n/a
49	RAD21	chr10:54073832-54074801	MCF-7	breast:	n/a	chr10:54074080-54074090 chr10:54074078-54074091
50	CTCF	chr10:54074640-54074790	SAEC	small airway:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:54074743-54074793	LNCaP	prostate:	n/a
2	chr10:54074743-54074793	AG04449	skin:	fetal
3	chr10:54074743-54074793	PANC-1	pancreas:	n/a
4	chr10:54074743-54074793	GM12892	blood:	n/a
5	chr10:54074743-54074793	NT2-D1	testis:	n/a
6	chr10:54074743-54074793	HRCEpiC	kidney:	n/a
7	chr10:54074743-54074793	AG10803	skin:	n/a
8	chr10:54074743-54074793	HRE	kidney:	n/a
9	chr10:54074743-54074793	T-47D	breast:	n/a
10	chr10:54074743-54074793	ECC-1	luminal epithelium:	n/a
11	chr10:54074743-54074793	K562	blood:	n/a
12	chr10:54074743-54074793	GM12891	blood:	n/a
13	chr10:54074743-54074793	SK-N-SH	brain:	n/a
14	chr10:54074743-54074793	ProgFib	skin:	n/a
15	chr10:54074743-54074793	AG04450	lung:	fetal
16	chr10:54074743-54074793	IMR90	lung:	fetal
17	chr10:54074743-54074793	HNPCEpiC	eye:	n/a
18	chr10:54074743-54074793	HUVEC	blood vessel:	n/a
19	chr10:54074743-54074793	H1-hESC	embryonic stem cell:	embryo
20	chr10:54074743-54074793	MCF10A-Er-Src	breast:	n/a
21	chr10:54074743-54074793	CMK	blood:	n/a
22	chr10:54074743-54074793	HCPEpiC	choroid plexus:	n/a
23	chr10:54074743-54074793	RPTEC	kidney:	n/a
24	chr10:54074743-54074793	AG09319	gingival:	n/a
25	chr10:54074743-54074793	HRPEpiC	eye:	n/a
26	chr10:54074743-54074793	MCF-7	breast:	n/a
27	chr10:54074743-54074793	PrEC	prostate:	n/a
28	chr10:54074743-54074793	A549	lung:	n/a
29	chr10:54074743-54074793	ovcar-3	ovarian:	n/a
30	chr10:54074743-54074793	NB4	blood:	n/a
31	chr10:54074743-54074793	HCT-116	colon:	n/a
32	chr10:54074743-54074793	HepG2	liver:	n/a
33	chr10:54074743-54074793	HPAEpiC	pulmonary alveolar:	n/a
34	chr10:54074743-54074793	BJ	skin:	n/a
35	chr10:54074743-54074793	Hela-S3	cervix:	n/a
36	chr10:54074743-54074793	GM06990	blood:	n/a
37	chr10:54074743-54074793	HCF	heart:	n/a
38	chr10:54074743-54074793	SK-N-SH_RA	brain:	n/a
39	chr10:54074743-54074793	GM12878	blood:	n/a
40	chr10:54074743-54074793	NH-A	brain:	n/a
41	chr10:54074743-54074793	Hepatocyte	liver:	n/a
42	chr10:54074743-54074793	PFSK-1	brain:	n/a
43	chr10:54074743-54074793	HEK293	kidney:	embryo
44	chr10:54074743-54074793	HL-60	blood:	n/a
45	chr10:54074743-54074793	HIPEpiC	eye:	n/a
46	chr10:54074743-54074793	Jurkat	blood:	n/a
47	chr10:54074743-54074793	SAEC	small airway:	n/a
48	chr10:54074743-54074793	GM19239	blood:	n/a
49	chr10:54074743-54074793	HAEpiC	amniotic membrane:	n/a
50	chr10:54074743-54074793	SKMC	muscle:	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:54065577..54083492-chr10:54193846..54218961,120	MCF-7	breast:
2	chr10:54073525..54075924-chr10:54146848..54149629,2	MCF-7	breast:
3	chr10:54073396..54076476-chr10:54227833..54231095,3	MCF-7	breast:
4	chr10:54073032..54076598-chr10:54229475..54234592,10	MCF-7	breast:
5	chr10:54071324..54082180-chr10:54192987..54217560,81	MCF-7	breast:

Variant related genes	Relation type
DKK1	TF binding region
PRKG1-AS1	TF binding region
DKK1	CpG island
PRKG1-AS1	CpG island
ENSG00000231131	Chromatin interaction
ENSG00000213657	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10733905	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10824381	0.86[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap]
rs11001560	0.93[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7087520	0.87[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv1045692	chr10:53301450-54086823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv895399	chr10:53900872-54219820	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv895400	chr10:54073294-54094359	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54072600-54075000	Active TSS	A549	lung
2	chr10:54072800-54074800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
3	chr10:54072800-54074800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
4	chr10:54072800-54075200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr10:54072800-54075200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:54072800-54075800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:54072800-54075800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:54073000-54074800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
9	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:54073000-54074800	Bivalent/Poised TSS	Aorta	Aorta
11	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
12	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
13	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
14	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
15	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
16	chr10:54073000-54074800	Enhancers	Spleen	Spleen
17	chr10:54073000-54075000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr10:54073000-54075800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:54073200-54074800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
20	chr10:54073200-54074800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
21	chr10:54073200-54074800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
22	chr10:54073200-54074800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
23	chr10:54073200-54074800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
24	chr10:54073200-54074800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
25	chr10:54073200-54074800	Active TSS	Psoas Muscle	Psoas
26	chr10:54073200-54075800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:54073400-54074800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr10:54073400-54074800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
29	chr10:54073400-54074800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
30	chr10:54073400-54075000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:54073400-54075200	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr10:54073400-54075400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr10:54073400-54075600	Active TSS	Brain Cingulate Gyrus	brain
34	chr10:54073400-54075800	Active TSS	HSMM	muscle
35	chr10:54073400-54075800	Active TSS	NHDF-Ad	bronchial
36	chr10:54073400-54076000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr10:54073400-54076200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr10:54073400-54076600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:54073600-54074800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr10:54073600-54075200	Active TSS	HMEC	breast
41	chr10:54073600-54075400	Active TSS	HUVEC	blood vessel
42	chr10:54073600-54075600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:54073600-54075600	Active TSS	HSMMtube	muscle
44	chr10:54073600-54075800	Active TSS	NH-A	brain
45	chr10:54073600-54075800	Active TSS	NHLF	lung
46	chr10:54073600-54077000	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr10:54073800-54074800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr10:54073800-54074800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
49	chr10:54073800-54075000	Active TSS	Hela-S3	cervix
50	chr10:54073800-54075000	Active TSS	NHEK	skin

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