Variant report

Variant	rs28616696
Chromosome Location	chr10:99188252-99188253
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	chr10:99188010-99188785	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr10:99187978-99188763	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr10:99188037-99188646	GM12892	blood:	n/a	n/a
4	ELF1	chr10:99188249-99188518	K562	blood:	n/a	chr10:99188418-99188429 chr10:99188418-99188429 chr10:99188419-99188428 chr10:99188417-99188430
5	POLR2A	chr10:99188032-99188587	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr10:99188016-99188802	HepG2	liver:	n/a	n/a
7	ELF1	chr10:99188110-99188612	GM12878	blood:	n/a	chr10:99188418-99188429 chr10:99188418-99188429 chr10:99188419-99188428 chr10:99188417-99188430
8	POLR2A	chr10:99188011-99188670	HL-60	blood:	n/a	n/a
9	POLR2A	chr10:99187971-99188854	U87	brain:	n/a	n/a
10	POLR2A	chr10:99186969-99188829	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:99186614-99188878	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr10:99187812-99188541	GM12878	blood:	n/a	n/a
13	STAT5A	chr10:99188161-99188756	GM12878	blood:	n/a	chr10:99188357-99188364
14	ATF2	chr10:99187559-99188272	GM12878	blood:	n/a	n/a
15	TBL1XR1	chr10:99188136-99188697	GM12878	blood:	n/a	n/a
16	TBP	chr10:99188111-99188481	GM12878	blood:	n/a	n/a
17	TAF1	chr10:99188236-99188484	GM12878	blood:	n/a	n/a
18	POLR2A	chr10:99185688-99189005	U87	brain:	n/a	n/a
19	POLR2A	chr10:99188142-99188731	HepG2	liver:	n/a	n/a
20	ELF1	chr10:99188153-99188609	K562	blood:	n/a	chr10:99188418-99188429 chr10:99188418-99188429 chr10:99188419-99188428 chr10:99188417-99188430
21	POLR2A	chr10:99187959-99188684	GM12878	blood:	n/a	n/a
22	POLR2A	chr10:99188151-99188601	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr10:99186726-99188896	U87	brain:	n/a	n/a
24	WRNIP1	chr10:99186193-99188754	GM12878	blood:	n/a	n/a
25	POLR2A	chr10:99187964-99188877	PANC-1	pancreas:	n/a	n/a
26	EBF1	chr10:99188177-99188486	GM12878	blood:	n/a	n/a
27	CHD1	chr10:99186327-99188375	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr10:99185340-99188887	GM12878	blood:	n/a	n/a
29	POLR2A	chr10:99187994-99188666	GM12892	blood:	n/a	n/a
30	POLR2A	chr10:99186776-99188842	K562	blood:	n/a	n/a
31	ELF1	chr10:99188248-99188565	HepG2	liver:	n/a	chr10:99188418-99188429 chr10:99188418-99188429 chr10:99188419-99188428 chr10:99188417-99188430
32	POLR2A	chr10:99185138-99188766	GM12891	blood:	n/a	n/a
33	POLR2A	chr10:99188055-99188704	GM12878	blood:	n/a	n/a
34	POLR2A	chr10:99187968-99188670	GM12892	blood:	n/a	n/a
35	CHD1	chr10:99188169-99188405	GM12878	blood:	n/a	n/a
36	POLR2A	chr10:99187962-99188854	U87	brain:	n/a	n/a
37	MTA3	chr10:99186687-99188621	GM12878	blood:	n/a	n/a
38	ELF1	chr10:99188215-99188611	HepG2	liver:	n/a	chr10:99188418-99188429 chr10:99188418-99188429 chr10:99188419-99188428 chr10:99188417-99188430
39	POLR2A	chr10:99188124-99188267	HepG2	liver:	n/a	n/a
40	YY1	chr10:99188232-99188539	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99158602..99162553-chr10:99184335..99188453,6	MCF-7	breast:
2	chr10:99185304..99188802-chr10:99201388..99207254,8	K562	blood:
3	chr10:99186982..99190152-chr10:99256815..99259689,3	K562	blood:
4	chr10:99178412..99183286-chr10:99183902..99188289,4	K562	blood:
5	chr10:99165495..99167483-chr10:99187813..99189704,2	K562	blood:
6	chr10:99185396..99188802-chr10:99202940..99206887,5	K562	blood:
7	chr10:99185211..99187426-chr10:99187705..99189889,2	MCF-7	breast:
8	chr10:99185991..99188987-chr10:99203440..99207245,5	MCF-7	breast:
9	chr10:99159614..99162570-chr10:99184923..99189339,4	K562	blood:
10	chr10:99187101..99190236-chr10:99202891..99208015,7	MCF-7	breast:
11	chr10:99176991..99182775-chr10:99183273..99189892,9	MCF-7	breast:
12	chr10:99158229..99164055-chr10:99184399..99190088,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224474	TF binding region
ENSG00000171314	Chromatin interaction
ENSG00000231970	Chromatin interaction
ENSG00000155229	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000165886	Chromatin interaction
ENSG00000224474	Chromatin interaction
ENSG00000052749	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000200737	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11189216	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189217	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266931	0.89[ASN][1000 genomes]
rs17112809	0.89[ASN][1000 genomes]
rs9943296	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467440	chr10:99134784-99204791	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv552025	chr10:99134784-99204791	Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 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	chr10:99185200-99188400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:99186000-99190200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:99186200-99188400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr10:99186200-99188600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr10:99186200-99188800	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr10:99186200-99189600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr10:99186400-99188800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr10:99186800-99188400	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr10:99186800-99188600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr10:99186800-99188600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:99186800-99188600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr10:99186800-99188600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:99186800-99188600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr10:99186800-99188600	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr10:99186800-99188600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr10:99186800-99188600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr10:99186800-99188600	Flanking Active TSS	Right Ventricle	heart
18	chr10:99186800-99188600	Flanking Active TSS	HUVEC	blood vessel
19	chr10:99186800-99188600	Flanking Active TSS	Osteobl	bone
20	chr10:99186800-99188800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr10:99186800-99188800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
22	chr10:99186800-99188800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:99186800-99188800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
24	chr10:99187000-99188400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
25	chr10:99187000-99188400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:99187000-99188400	Flanking Active TSS	Fetal Brain Female	brain
27	chr10:99187000-99188600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr10:99187000-99188600	Transcr. at gene 5' and 3'	NHEK	skin
29	chr10:99187000-99188800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
30	chr10:99187000-99188800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:99187000-99188800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
32	chr10:99187000-99188800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
33	chr10:99187000-99188800	Transcr. at gene 5' and 3'	A549	lung
34	chr10:99187000-99188800	Transcr. at gene 5' and 3'	K562	blood
35	chr10:99187000-99190600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
36	chr10:99187200-99188400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr10:99187200-99188600	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
38	chr10:99187200-99188600	Enhancers	Spleen	Spleen
39	chr10:99187200-99188600	Transcr. at gene 5' and 3'	HSMM	muscle
40	chr10:99187200-99188800	Transcr. at gene 5' and 3'	Hela-S3	cervix
41	chr10:99187200-99188800	Transcr. at gene 5' and 3'	HMEC	breast
42	chr10:99187400-99188600	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
43	chr10:99187400-99188600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr10:99187400-99188600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
45	chr10:99187400-99188600	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr10:99187400-99188600	Genic enhancers	Primary hematopoietic stem cells	blood
47	chr10:99187400-99188600	Enhancers	Placenta	Placenta
48	chr10:99187400-99188800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
49	chr10:99187400-99188800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr10:99187400-99188800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin

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