Variant report

Variant	rs16869509
Chromosome Location	chr8:103548632-103548633
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	NFATC1	chr8:103547887-103548699	GM12878	blood:	n/a	n/a
2	SIN3A	chr8:103547929-103549256	H1-hESC	embryonic stem cell:	n/a	n/a
3	STAT3	chr8:103548066-103548700	GM12878	blood:	n/a	n/a
4	MYC	chr8:103548046-103548798	H1-hESC	embryonic stem cell:	n/a	n/a
5	STAT1	chr8:103548049-103548636	GM12878	blood:	n/a	n/a
6	POU5F1	chr8:103548075-103548802	H1-hESC	embryonic stem cell:	n/a	chr8:103548368-103548382 chr8:103548368-103548382 chr8:103548432-103548446 chr8:103548432-103548446 chr8:103548368-103548382 chr8:103548367-103548381 chr8:103548450-103548464 chr8:103548431-103548445
7	POLR2A	chr8:103548350-103548744	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZEB1	chr8:103547886-103548703	GM12878	blood:	n/a	n/a
9	TEAD4	chr8:103547860-103548767	H1-hESC	embryonic stem cell:	n/a	n/a
10	POU2F2	chr8:103547899-103548837	GM12891	blood:	n/a	n/a
11	POLR2A	chr8:103548429-103548903	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr8:103547960-103548765	H1-hESC	embryonic stem cell:	n/a	n/a
13	JUND	chr8:103548476-103548661	H1-hESC	embryonic stem cell:	n/a	n/a
14	MYC	chr8:103547902-103548644	MCF10A-Er-Src	breast:	n/a	n/a
15	SMC3	chr8:103547914-103548772	GM12878	blood:	n/a	chr8:103548161-103548171
16	CUX1	chr8:103547951-103548721	GM12878	blood:	n/a	n/a
17	BCLAF1	chr8:103547756-103548686	GM12878	blood:	n/a	n/a
18	ATF2	chr8:103547563-103548901	GM12878	blood:	n/a	n/a
19	POLR2A	chr8:103547679-103548725	GM18951	blood:	n/a	n/a
20	TCF12	chr8:103547956-103548794	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr8:103548463-103548996	GM12878	blood:	n/a	n/a
22	TCF12	chr8:103547995-103548785	GM12878	blood:	n/a	n/a
23	TCF3	chr8:103548455-103548795	GM12878	blood:	n/a	n/a
24	PAX5	chr8:103547887-103548711	GM12878	blood:	n/a	n/a
25	FOXM1	chr8:103547803-103548795	GM12878	blood:	n/a	n/a
26	HDAC2	chr8:103547867-103548795	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAFK	chr8:103548487-103548855	Hela-S3	cervix:	n/a	chr8:103548579-103548595
28	ZNF143	chr8:103547944-103548707	H1-hESC	embryonic stem cell:	n/a	chr8:103548531-103548550
29	ATF2	chr8:103547869-103548776	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr8:103548460-103548715	H1-hESC	embryonic stem cell:	n/a	n/a
31	RCOR1	chr8:103547885-103548685	GM12878	blood:	n/a	n/a
32	SP1	chr8:103547820-103548840	H1-hESC	embryonic stem cell:	n/a	chr8:103548306-103548316
33	TCF7L2	chr8:103548033-103548808	Hela-S3	cervix:	n/a	n/a
34	TBL1XR1	chr8:103547932-103548743	GM12878	blood:	n/a	n/a
35	POU2F2	chr8:103547915-103548828	GM12878	blood:	n/a	n/a
36	FOXM1	chr8:103547549-103548844	GM12878	blood:	n/a	n/a
37	SP1	chr8:103547828-103548735	H1-hESC	embryonic stem cell:	n/a	chr8:103548306-103548316
38	MAX	chr8:103547899-103548831	H1-hESC	embryonic stem cell:	n/a	n/a
39	IKZF1	chr8:103547890-103548737	GM12878	blood:	n/a	n/a
40	RELA	chr8:103547896-103548765	GM12891	blood:	n/a	n/a
41	RAD21	chr8:103547971-103548717	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr8:103547796-103548917	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr8:103547920-103548727	GM19193	blood:	n/a	n/a
44	RELA	chr8:103547891-103548769	GM18951	blood:	n/a	n/a
45	POLR2A	chr8:103547527-103548826	GM12878	blood:	n/a	n/a
46	POLR2A	chr8:103547802-103548695	GM12892	blood:	n/a	n/a
47	PML	chr8:103547505-103548919	GM12878	blood:	n/a	n/a
48	RELA	chr8:103547583-103548824	GM18505	blood:	n/a	n/a
49	TCF12	chr8:103547697-103550461	A549	lung:	n/a	chr8:103548853-103548860
50	CHD2	chr8:103547875-103548801	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:103548290..103549858-chr8:103666660..103669466,2	K562	blood:
2	chr8:103437958..103439977-chr8:103547146..103549346,2	MCF-7	breast:
3	chr8:103547915..103550298-chr8:103554370..103557167,3	K562	blood:
4	chr8:103423156..103426710-chr8:103547734..103551186,4	MCF-7	breast:
5	chr8:103540698..103544207-chr8:103546696..103550142,4	MCF-7	breast:
6	chr8:103539619..103542009-chr8:103547137..103548824,2	MCF-7	breast:
7	chr8:103255266..103257268-chr8:103548486..103550242,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-1224P	TF binding region
ENSG00000246263	Chromatin interaction
ENSG00000253633	Chromatin interaction
ENSG00000104517	Chromatin interaction
ENSG00000155090	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1000672	0.81[JPT][hapmap]
rs16869534	0.82[AMR][1000 genomes]
rs34524601	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4734635	0.80[ASN][1000 genomes]
rs62523267	0.86[AMR][1000 genomes]
rs62524851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8180987	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1031769	chr8:103460754-103620283	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv539703	chr8:103460754-103620283	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv2762761	chr8:103492356-103625244	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv1831575	chr8:103498317-103585093	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1838972	chr8:103498317-103585093	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1024876	chr8:103512785-103576658	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3419415	chr8:103525141-103575507	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103541200-103549000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:103541800-103549800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr8:103543400-103549400	Weak transcription	K562	blood
4	chr8:103544000-103550600	Enhancers	Fetal Brain Male	brain
5	chr8:103546200-103549000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr8:103546200-103549200	Enhancers	Osteobl	bone
7	chr8:103546200-103550200	Enhancers	NHDF-Ad	bronchial
8	chr8:103546400-103548800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr8:103546400-103550600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr8:103546600-103549000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr8:103546600-103550200	Enhancers	Thymus	Thymus
12	chr8:103546600-103550200	Enhancers	NHLF	lung
13	chr8:103546600-103550400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr8:103546600-103550600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr8:103546600-103550600	Enhancers	Fetal Thymus	thymus
16	chr8:103546800-103550000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr8:103546800-103551400	Weak transcription	Right Ventricle	heart
18	chr8:103547000-103549000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:103547000-103549600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr8:103547000-103556800	Weak transcription	Spleen	Spleen
21	chr8:103547200-103548800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr8:103547400-103548800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr8:103547400-103549000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr8:103547400-103549600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr8:103547400-103550200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr8:103547600-103548800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr8:103547600-103549000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr8:103547600-103549000	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr8:103547600-103549000	Enhancers	NH-A	brain
30	chr8:103547600-103549200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr8:103547600-103550000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr8:103547600-103550000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr8:103547600-103550200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr8:103547600-103550400	Enhancers	NHEK	skin
35	chr8:103547600-103550600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr8:103547600-103550600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr8:103547800-103548800	Enhancers	Primary T cells from cord blood	blood
38	chr8:103547800-103548800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr8:103547800-103549600	Enhancers	Psoas Muscle	Psoas
40	chr8:103547800-103550200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr8:103547800-103550200	Enhancers	Brain Hippocampus Middle	brain
42	chr8:103547800-103550200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr8:103547800-103550400	Flanking Active TSS	A549	lung
44	chr8:103547800-103550800	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr8:103548000-103548800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr8:103548000-103548800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr8:103548000-103548800	Enhancers	Aorta	Aorta
48	chr8:103548000-103548800	Enhancers	Small Intestine	intestine
49	chr8:103548000-103548800	Enhancers	Stomach Smooth Muscle	stomach
50	chr8:103548000-103549000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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