Variant report

Variant	rs16899667
Chromosome Location	chr8:125550551-125550552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:163)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:163 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:125550533-125551637	HUVEC	blood vessel:	n/a	n/a
2	MXI1	chr8:125550520-125551790	GM12878	blood:	n/a	n/a
3	MXI1	chr8:125550232-125551951	IMR90	lung:	n/a	n/a
4	CBX3	chr8:125550241-125551682	K562	blood:	n/a	n/a
5	ELK1	chr8:125550551-125550806	K562	blood:	n/a	n/a
6	POLR2A	chr8:125550509-125551801	GM19193	blood:	n/a	n/a
7	POLR2A	chr8:125550511-125551898	K562	blood:	n/a	n/a
8	MAX	chr8:125550533-125551823	SK-N-SH	brain:	n/a	chr8:125550935-125550942
9	POLR2A	chr8:125550374-125551791	K562	blood:	n/a	n/a
10	TBP	chr8:125550495-125551982	K562	blood:	n/a	n/a
11	MYC	chr8:125550337-125551798	K562	blood:	n/a	chr8:125550399-125550408 chr8:125550935-125550942
12	RUNX3	chr8:125550544-125551842	GM12878	blood:	n/a	n/a
13	POLR2A	chr8:125550246-125551878	GM12878	blood:	n/a	n/a
14	POLR2A	chr8:125550278-125551649	HepG2	liver:	n/a	n/a
15	MYC	chr8:125550469-125551892	K562	blood:	n/a	chr8:125550935-125550942
16	POLR2A	chr8:125550489-125550969	H1-hESC	embryonic stem cell:	n/a	n/a
17	HEY1	chr8:125550541-125551680	HepG2	liver:	n/a	n/a
18	FOXM1	chr8:125550501-125551032	GM12878	blood:	n/a	n/a
19	POLR2A	chr8:125550506-125551756	PFSK-1	brain:	n/a	n/a
20	JUN	chr8:125550369-125551582	K562	blood:	n/a	chr8:125550400-125550408 chr8:125550396-125550407 chr8:125550401-125550408 chr8:125550400-125550408 chr8:125550399-125550409
21	TRIM28	chr8:125550504-125551968	K562	blood:	n/a	n/a
22	POLR2A	chr8:125550232-125551685	U87	brain:	n/a	n/a
23	POLR2A	chr8:125550380-125551850	K562	blood:	n/a	n/a
24	POLR2A	chr8:125550202-125551784	GM12878	blood:	n/a	n/a
25	TAF1	chr8:125550550-125551692	GM12878	blood:	n/a	n/a
26	POLR2A	chr8:125550269-125551783	K562	blood:	n/a	n/a
27	MYC	chr8:125550275-125552110	K562	blood:	n/a	chr8:125550399-125550408 chr8:125550935-125550942
28	CTCF	chr8:125550462-125551041	T-47D	breast:	n/a	n/a
29	MAX	chr8:125550232-125552052	HCT-116	colon:	n/a	chr8:125550399-125550408 chr8:125550935-125550942
30	TCF12	chr8:125550493-125552030	A549	lung:	n/a	n/a
31	BRCA1	chr8:125550497-125551967	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr8:125550353-125552164	HepG2	liver:	n/a	n/a
33	RAD21	chr8:125550479-125551037	MCF-7	breast:	n/a	chr8:125550671-125550680
34	POLR2A	chr8:125549583-125551914	GM12891	blood:	n/a	n/a
35	POLR2A	chr8:125550328-125552237	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr8:125550257-125550978	GM12891	blood:	n/a	n/a
37	MXI1	chr8:125549508-125552974	SK-N-SH	brain:	n/a	n/a
38	RELA	chr8:125550548-125551669	GM19099	blood:	n/a	n/a
39	POLR2A	chr8:125549444-125552363	SK-N-MC	brain:	n/a	n/a
40	SMC3	chr8:125550483-125551622	Hela-S3	cervix:	n/a	n/a
41	SIN3AK20	chr8:125550247-125552061	MCF-7	breast:	n/a	n/a
42	POLR2A	chr8:125550359-125551803	PANC-1	pancreas:	n/a	n/a
43	MAFK	chr8:125550348-125550552	HepG2	liver:	n/a	n/a
44	MAX	chr8:125550175-125551937	MCF-7	breast:	n/a	chr8:125550399-125550408 chr8:125550935-125550942
45	MAX	chr8:125550466-125551797	Hela-S3	cervix:	n/a	chr8:125550935-125550942
46	POLR2A	chr8:125550338-125551815	HUVEC	blood vessel:	n/a	n/a
47	ELF1	chr8:125550368-125551890	MCF-7	breast:	n/a	chr8:125551316-125551325 chr8:125551313-125551326
48	SIN3AK20	chr8:125550433-125551863	HCT-116	colon:	n/a	n/a
49	CTCF	chr8:125550517-125550914	A549	lung:	n/a	n/a
50	MTA3	chr8:125550113-125551957	GM12878	blood:	n/a	n/a

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:125547667..125554911-chr8:125566055..125572382,17	MCF-7	breast:
2	chr8:125548205..125551096-chr8:125575812..125578141,2	MCF-7	breast:
3	chr8:125459427..125466261-chr8:125549985..125555147,10	K562	blood:
4	chr8:125549492..125551989-chr8:125824960..125829256,5	K562	blood:
5	chr8:125547520..125551844-chr8:126101419..126105683,3	MCF-7	breast:
6	chr8:125550147..125552790-chr8:125567789..125570449,2	MCF-7	breast:
7	chr8:125548510..125551607-chr8:125929970..125932882,3	MCF-7	breast:
8	chr8:125515035..125519543-chr8:125547357..125551225,5	MCF-7	breast:
9	chr1:151170674..151172337-chr8:125550185..125552873,2	MCF-7	breast:
10	chr8:125549831..125551409-chr8:125739286..125741874,2	MCF-7	breast:
11	chr12:69978648..69980744-chr8:125549936..125551703,2	MCF-7	breast:
12	chr8:125461480..125466921-chr8:125547850..125552862,10	MCF-7	breast:
13	chr8:125498976..125500980-chr8:125550117..125552878,2	MCF-7	breast:
14	chr8:125461877..125466400-chr8:125548792..125551961,4	MCF-7	breast:
15	chr8:125549460..125555106-chr8:125573452..125578755,9	MCF-7	breast:
16	chr8:125491802..125498170-chr8:125548148..125552034,10	MCF-7	breast:
17	chr8:125548946..125551897-chr8:126103590..126105323,2	MCF-7	breast:
18	chr8:125550551..125551259-chr8:125561525..125562151,2	MCF-7	breast:
19	chr8:125484298..125489708-chr8:125549185..125553061,9	MCF-7	breast:
20	chr8:125483604..125491110-chr8:125548591..125554086,23	K562	blood:
21	chr8:125549374..125552995-chr8:126009841..126015179,7	MCF-7	breast:
22	chr8:125494945..125497543-chr8:125548660..125551608,2	K562	blood:
23	chr8:125482386..125490832-chr8:125532319..125553620,55	MCF-7	breast:
24	chr8:125548570..125552806-chr8:125825742..125828762,4	K562	blood:
25	chr8:125484053..125491713-chr8:125548138..125554442,21	K562	blood:
26	chr8:125460680..125466261-chr8:125549985..125555147,10	K562	blood:
27	chr8:125549873..125552042-chr8:125579435..125582392,2	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFB9	TF binding region
ENSG00000164961	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000156831	Chromatin interaction
ENSG00000170873	Chromatin interaction
ENSG00000250428	Chromatin interaction
ENSG00000104549	Chromatin interaction
ENSG00000253513	Chromatin interaction
ENSG00000183665	Chromatin interaction
ENSG00000255491	Chromatin interaction
ENSG00000245149	Chromatin interaction
ENSG00000253106	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000166226	Chromatin interaction
ENSG00000143398	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11986571	1.00[AMR][1000 genomes]
rs13276295	0.85[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16899667	BIK	trans	lymphoblastoid	seeQTL
rs16899667	SLC30A8	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125504000-125550800	Weak transcription	Spleen	Spleen
2	chr8:125520000-125550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:125540200-125550600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:125549600-125550600	Flanking Active TSS	Hela-S3	cervix
5	chr8:125549600-125550800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr8:125549600-125550800	Enhancers	Small Intestine	intestine
7	chr8:125549600-125551000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr8:125549600-125551000	Flanking Active TSS	Dnd41	blood
9	chr8:125549600-125551000	Flanking Active TSS	HUVEC	blood vessel
10	chr8:125549600-125552400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr8:125549800-125550600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr8:125549800-125550600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr8:125549800-125550600	Flanking Active TSS	HMEC	breast
14	chr8:125549800-125550800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:125549800-125550800	Flanking Active TSS	Osteobl	bone
16	chr8:125549800-125551000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr8:125549800-125552600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr8:125549800-125552600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr8:125550000-125550600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr8:125550000-125550600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr8:125550000-125550600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr8:125550000-125550600	Enhancers	Primary B cells from peripheral blood	blood
23	chr8:125550000-125550600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr8:125550000-125550600	Flanking Active TSS	HSMMtube	muscle
25	chr8:125550000-125550800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr8:125550000-125550800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr8:125550000-125550800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr8:125550000-125550800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr8:125550000-125550800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr8:125550000-125550800	Flanking Active TSS	NH-A	brain
31	chr8:125550000-125551000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr8:125550000-125551200	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr8:125550000-125552400	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr8:125550000-125552600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr8:125550000-125552600	Active TSS	K562	blood
36	chr8:125550000-125553200	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr8:125550200-125550600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
38	chr8:125550200-125550600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr8:125550200-125550600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr8:125550200-125550600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr8:125550200-125550600	Flanking Active TSS	Fetal Brain Female	brain
42	chr8:125550200-125550600	Flanking Active TSS	Fetal Intestine Large	intestine
43	chr8:125550200-125550800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr8:125550200-125550800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr8:125550200-125550800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr8:125550200-125550800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr8:125550200-125550800	Flanking Active TSS	Liver	Liver
48	chr8:125550200-125550800	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr8:125550200-125550800	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr8:125550200-125550800	Flanking Active TSS	Brain Germinal Matrix	brain

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