Variant report

Variant	rs7520077
Chromosome Location	chr1:10533425-10533426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr1:10531760-10533473	K562	blood:	n/a	n/a
2	POLR2A	chr1:10532073-10533485	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:10533203-10533553	K562	blood:	n/a	n/a
4	POLR2A	chr1:10531843-10533584	GM12892	blood:	n/a	n/a
5	MAX	chr1:10533243-10533512	K562	blood:	n/a	n/a
6	POLR2A	chr1:10531884-10533592	GM15510	blood:	n/a	n/a
7	POLR2A	chr1:10532082-10533539	GM12891	blood:	n/a	n/a
8	JUND	chr1:10533305-10533658	K562	blood:	n/a	n/a
9	POLR2A	chr1:10533162-10533772	GM12892	blood:	n/a	n/a
10	MAX	chr1:10533250-10533744	K562	blood:	n/a	n/a
11	MYC	chr1:10531703-10533880	K562	blood:	n/a	n/a
12	EGR1	chr1:10533181-10533635	K562	blood:	n/a	n/a
13	POLR2A	chr1:10532113-10533596	K562	blood:	n/a	n/a
14	MAX	chr1:10533338-10533631	K562	blood:	n/a	n/a
15	TAF1	chr1:10533207-10533626	K562	blood:	n/a	n/a
16	E2F6	chr1:10533299-10533492	K562	blood:	n/a	n/a
17	YY1	chr1:10533257-10533730	K562	blood:	n/a	n/a
18	SREBP1	chr1:10531974-10533485	GM12878	blood:	n/a	n/a
19	HEY1	chr1:10533143-10533676	K562	blood:	n/a	n/a
20	POLR2A	chr1:10531885-10533665	GM18505	blood:	n/a	n/a
21	ARID3A	chr1:10532496-10533506	K562	blood:	n/a	n/a
22	RCOR1	chr1:10533305-10533593	K562	blood:	n/a	n/a
23	POLR2A	chr1:10532216-10533609	K562	blood:	n/a	n/a
24	POLR2A	chr1:10533204-10533505	K562	blood:	n/a	n/a
25	YY1	chr1:10533262-10533581	K562	blood:	n/a	n/a
26	EP300	chr1:10532363-10533545	K562	blood:	n/a	chr1:10533036-10533050 chr1:10533147-10533157 chr1:10532940-10532949
27	POLR2A	chr1:10531936-10533430	K562	blood:	n/a	n/a
28	POLR2A	chr1:10532020-10533635	K562	blood:	n/a	n/a
29	POLR2A	chr1:10533170-10533732	K562	blood:	n/a	n/a
30	TEAD4	chr1:10531517-10533595	K562	blood:	n/a	n/a
31	POLR2A	chr1:10531918-10533668	GM19099	blood:	n/a	n/a
32	EGR1	chr1:10533231-10533514	K562	blood:	n/a	n/a
33	TAF1	chr1:10533250-10533488	K562	blood:	n/a	n/a
34	HDAC2	chr1:10533259-10533580	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10528950..10534210-chr1:10534257..10537658,6	K562	blood:
2	chr1:10457403..10461622-chr1:10531171..10536559,7	K562	blood:
3	chr1:10517930..10519443-chr1:10532494..10534240,2	K562	blood:
4	chr1:10489993..10493018-chr1:10531254..10535234,5	MCF-7	breast:
5	chr1:10457604..10459438-chr1:10532689..10534375,2	K562	blood:
6	chr1:10490607..10494447-chr1:10532445..10535163,5	K562	blood:
7	chr1:10488008..10492443-chr1:10531123..10534892,8	K562	blood:
8	chr1:10494601..10496370-chr1:10532163..10533964,2	K562	blood:

No data

Variant related genes	Relation type
PEX14	TF binding region
DFFA	TF binding region
ENSG00000175279	Chromatin interaction
ENSG00000203469	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000271989	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11121574	0.91[AFR][1000 genomes]
rs11121575	0.91[AFR][1000 genomes]
rs11121576	0.88[AFR][1000 genomes]
rs11121578	0.91[AFR][1000 genomes]
rs11539793	1.00[CHD][hapmap]
rs12131785	1.00[CHD][hapmap]
rs6667629	1.00[ASW][hapmap];0.94[LWK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs7532322	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 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	chr1:10532000-10534200	Active TSS	GM12878-XiMat	blood
2	chr1:10532200-10533600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:10532200-10533600	Active TSS	K562	blood
4	chr1:10532600-10534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:10532600-10534600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:10532600-10535000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:10532800-10533600	Flanking Active TSS	Primary B cells from peripheral blood	blood
8	chr1:10532800-10535000	Weak transcription	Spleen	Spleen
9	chr1:10533000-10533800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:10533000-10534600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:10533000-10534600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:10533000-10534600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:10533000-10534600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:10533000-10534600	Weak transcription	Brain Germinal Matrix	brain
15	chr1:10533000-10534600	Weak transcription	Fetal Brain Female	brain
16	chr1:10533000-10534600	Weak transcription	Left Ventricle	heart
17	chr1:10533000-10534600	Weak transcription	Ovary	ovary
18	chr1:10533000-10534600	Weak transcription	Pancreas	Pancrea
19	chr1:10533000-10534600	Weak transcription	Right Ventricle	heart
20	chr1:10533000-10534600	Weak transcription	Small Intestine	intestine
21	chr1:10533000-10534600	Weak transcription	HSMM	muscle
22	chr1:10533000-10534600	Weak transcription	HUVEC	blood vessel
23	chr1:10533000-10534800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:10533000-10534800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:10533000-10534800	Weak transcription	Esophagus	oesophagus
26	chr1:10533000-10534800	Weak transcription	Gastric	stomach
27	chr1:10533000-10534800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:10533000-10535000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:10533000-10535000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:10533000-10535000	Weak transcription	Aorta	Aorta
31	chr1:10533000-10535000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:10533200-10533600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr1:10533200-10533600	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr1:10533200-10533600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:10533200-10533600	Enhancers	Fetal Thymus	thymus
36	chr1:10533200-10533600	Enhancers	Hela-S3	cervix
37	chr1:10533200-10533800	Enhancers	Primary B cells from cord blood	blood
38	chr1:10533200-10533800	Enhancers	Primary T cells fromperipheralblood	blood
39	chr1:10533200-10533800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:10533200-10534000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr1:10533200-10534200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:10533200-10534200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:10533200-10534200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:10533200-10534200	Weak transcription	A549	lung
45	chr1:10533200-10534200	Weak transcription	NHDF-Ad	bronchial
46	chr1:10533200-10534400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:10533200-10534400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:10533200-10534400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:10533200-10534400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:10533200-10534400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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