Variant report

Variant	rs28999671
Chromosome Location	chr8:103250443-103250444
allele	C/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	CHD1	chr8:103248792-103252333	IMR90	lung:	n/a	chr8:103251203-103251213
2	TBP	chr8:103249997-103251247	GM12878	blood:	n/a	n/a
3	POU2F2	chr8:103250380-103252280	GM12878	blood:	n/a	chr8:103251205-103251217 chr8:103251721-103251733
4	MAX	chr8:103250361-103252737	MCF-7	breast:	n/a	chr8:103252521-103252530 chr8:103252519-103252532 chr8:103252520-103252531 chr8:103252519-103252532 chr8:103252520-103252530 chr8:103252519-103252532 chr8:103252520-103252531 chr8:103252520-103252530 chr8:103252520-103252531
5	MXI1	chr8:103249696-103252738	SK-N-SH	brain:	n/a	chr8:103252520-103252529 chr8:103252520-103252529
6	MAZ	chr8:103250428-103252560	IMR90	lung:	n/a	chr8:103252521-103252530 chr8:103252519-103252532 chr8:103252520-103252531 chr8:103252519-103252532 chr8:103252520-103252530 chr8:103252519-103252532 chr8:103252520-103252531 chr8:103252520-103252530 chr8:103252520-103252531
7	POLR2A	chr8:103250410-103251193	GM12891	blood:	n/a	n/a
8	HCFC1	chr8:103249628-103252196	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr8:103250379-103251262	GM12892	blood:	n/a	n/a
10	GABPA	chr8:103250402-103252188	MCF-7	breast:	n/a	chr8:103251205-103251214 chr8:103251488-103251497 chr8:103251573-103251582
11	CHD1	chr8:103250412-103250528	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr8:103248763-103252162	MCF10A-Er-Src	breast:	n/a	n/a
13	SIN3AK20	chr8:103250435-103251279	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr8:103250355-103252269	GM18505	blood:	n/a	n/a
15	POLR2A	chr8:103250362-103251215	GM12892	blood:	n/a	n/a
16	POLR2A	chr8:103248979-103252107	IMR90	lung:	n/a	n/a
17	POLR2A	chr8:103249704-103252596	GM12878	blood:	n/a	n/a
18	SIN3AK20	chr8:103250266-103252390	MCF-7	breast:	n/a	n/a
19	MXI1	chr8:103250161-103252101	Hela-S3	cervix:	n/a	n/a
20	SIN3A	chr8:103250340-103252178	H1-hESC	embryonic stem cell:	n/a	chr8:103251555-103251568
21	CHD1	chr8:103248610-103251204	GM12878	blood:	n/a	n/a
22	POLR2A	chr8:103248725-103251275	GM12891	blood:	n/a	n/a
23	POLR2A	chr8:103250379-103252183	GM18526	blood:	n/a	n/a
24	POLR2A	chr8:103248842-103251256	GM12878	blood:	n/a	n/a
25	BRCA1	chr8:103250429-103252142	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr8:103250361-103252249	GM19099	blood:	n/a	n/a
27	PML	chr8:103250413-103252469	GM12878	blood:	n/a	n/a
28	HDAC2	chr8:103250391-103252472	MCF-7	breast:	n/a	n/a
29	MTA3	chr8:103250151-103252388	GM12878	blood:	n/a	n/a
30	MXI1	chr8:103250000-103252677	GM12878	blood:	n/a	chr8:103252520-103252529 chr8:103252520-103252529
31	SIN3AK20	chr8:103250261-103252608	MCF-7	breast:	n/a	n/a
32	TCF12	chr8:103250431-103251447	A549	lung:	n/a	n/a
33	POLR2A	chr8:103248887-103252665	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr8:103250350-103252819	Raji	blood:	n/a	n/a
35	RUNX3	chr8:103250420-103252408	GM12878	blood:	n/a	n/a
36	POLR2A	chr8:103250377-103251239	GM12891	blood:	n/a	n/a
37	MXI1	chr8:103250066-103252566	IMR90	lung:	n/a	chr8:103252520-103252529 chr8:103252520-103252529
38	POLR2A	chr8:103250373-103252321	GM12878	blood:	n/a	n/a
39	POLR2A	chr8:103250422-103252176	GM19193	blood:	n/a	n/a
40	POLR2A	chr8:103250336-103251201	GM12891	blood:	n/a	n/a
41	POLR2A	chr8:103250356-103252157	GM12892	blood:	n/a	n/a
42	REST	chr8:103250354-103252371	H1-neurons	neurons:	n/a	chr8:103250862-103250870 chr8:103252012-103252021 chr8:103251555-103251568 chr8:103252000-103252013 chr8:103251204-103251217 chr8:103250818-103250831 chr8:103251170-103251180
43	POLR2A	chr8:103250355-103251331	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:103250357..103253420-chr8:103818570..103821747,5	MCF-7	breast:
2	chr8:102504608..102506883-chr8:103249593..103253284,4	MCF-7	breast:
3	chr8:103249647..103255113-chr8:103258766..103269094,16	K562	blood:
4	chr8:102505170..102507558-chr8:103249030..103250734,2	MCF-7	breast:
5	chr8:103250055..103252401-chr8:103423281..103425578,3	K562	blood:
6	chr6:126307907..126309585-chr8:103249281..103251409,2	MCF-7	breast:
7	chr8:103248364..103250740-chr8:103821721..103824052,2	MCF-7	breast:
8	chr17:42277839..42278417-chr8:103250218..103250798,2	Hela-S3	cervix:
9	chr8:103249660..103252444-chr8:103873911..103876787,3	K562	blood:
10	chr12:120729699..120731594-chr8:103249371..103251241,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246263	TF binding region
ENSG00000066651	Chromatin interaction
ENSG00000272037	Chromatin interaction
ENSG00000104517	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000253669	Chromatin interaction
ENSG00000254024	Chromatin interaction
ENSG00000083307	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10505019	0.80[ASN][1000 genomes]
rs1052069	0.80[ASN][1000 genomes]
rs1052071	0.80[ASN][1000 genomes]
rs11774420	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11774459	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11776865	0.80[ASN][1000 genomes]
rs11777942	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11778107	0.93[ASN][1000 genomes]
rs11783467	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784180	0.93[ASN][1000 genomes]
rs11784534	0.87[ASN][1000 genomes]
rs11785514	0.80[ASN][1000 genomes]
rs11786397	0.87[ASN][1000 genomes]
rs16869269	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16869276	0.93[ASN][1000 genomes]
rs16869282	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869295	0.93[ASN][1000 genomes]
rs16918482	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2387995	0.93[ASN][1000 genomes]
rs28928571	0.93[ASN][1000 genomes]
rs28928592	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28928597	0.93[ASN][1000 genomes]
rs28999676	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28999706	0.93[ASN][1000 genomes]
rs29000274	0.93[ASN][1000 genomes]
rs29000286	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs29000294	0.80[ASN][1000 genomes]
rs3735720	0.80[ASN][1000 genomes]
rs3735721	0.80[ASN][1000 genomes]
rs3735722	0.93[ASN][1000 genomes]
rs3907099	0.80[ASN][1000 genomes]
rs4329248	0.87[ASN][1000 genomes]
rs5005121	0.80[ASN][1000 genomes]
rs57901015	0.87[ASN][1000 genomes]
rs60604862	0.80[ASN][1000 genomes]
rs7836046	0.93[ASN][1000 genomes]
rs7841131	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv891242	chr8:103210971-103282418	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv891243	chr8:103219629-103292724	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 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	chr8:103241400-103250600	Weak transcription	Spleen	Spleen
2	chr8:103248000-103250800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr8:103248400-103250600	Flanking Active TSS	Osteobl	bone
4	chr8:103248600-103250600	Flanking Active TSS	Brain Hippocampus Middle	brain
5	chr8:103248600-103250800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr8:103248600-103250800	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr8:103248600-103250800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr8:103248800-103250600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr8:103248800-103250600	Flanking Active TSS	NHEK	skin
10	chr8:103248800-103250800	Flanking Active TSS	HUVEC	blood vessel
11	chr8:103248800-103252400	Active TSS	Aorta	Aorta
12	chr8:103249000-103250800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr8:103249000-103250800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr8:103249000-103251000	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr8:103249000-103251000	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr8:103249000-103251000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr8:103249200-103250600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr8:103249200-103250600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr8:103249200-103251000	Active TSS	Right Atrium	heart
20	chr8:103249200-103252200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr8:103249200-103252200	Active TSS	NHLF	lung
22	chr8:103249400-103250600	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr8:103249400-103250800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr8:103249400-103250800	Flanking Active TSS	Dnd41	blood
25	chr8:103249400-103252200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr8:103249400-103252200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr8:103249400-103252200	Active TSS	HSMM	muscle
28	chr8:103249400-103252400	Active TSS	Psoas Muscle	Psoas
29	chr8:103249400-103252800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr8:103249400-103252800	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr8:103249600-103250600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr8:103249600-103250600	Flanking Active TSS	Hela-S3	cervix
33	chr8:103249600-103250800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:103249600-103250800	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr8:103249600-103250800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr8:103249600-103250800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr8:103249600-103252200	Active TSS	GM12878-XiMat	blood
38	chr8:103249600-103252200	Active TSS	NHDF-Ad	bronchial
39	chr8:103249600-103252400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr8:103249600-103253200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr8:103249800-103250600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr8:103249800-103250600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr8:103249800-103250600	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr8:103249800-103250600	Flanking Active TSS	Fetal Brain Male	brain
45	chr8:103249800-103250600	Flanking Active TSS	Fetal Brain Female	brain
46	chr8:103249800-103250800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr8:103249800-103250800	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr8:103249800-103251000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr8:103249800-103251800	Active TSS	HMEC	breast
50	chr8:103249800-103252000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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