Variant report

Variant	rs12089548
Chromosome Location	chr1:150780959-150780960
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150780358-150781259	U87	brain:	n/a	n/a
2	POLR2A	chr1:150780497-150781050	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr1:150780584-150781093	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:150780702-150781079	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:150780709-150781051	Hela-S3	cervix:	n/a	n/a
6	FOSL2	chr1:150780610-150781035	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:150780842-150780968	K562	blood:	n/a	n/a
8	POLR2A	chr1:150780069-150781792	K562	blood:	n/a	n/a
9	POLR2A	chr1:150780838-150781042	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr1:150780232-150781057	U87	brain:	n/a	n/a
11	POLR2A	chr1:150780424-150781184	U87	brain:	n/a	n/a
12	POLR2A	chr1:150780479-150780983	PFSK-1	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150779291..150781180-chr1:150784227..150787241,3	K562	blood:
2	chr1:150668066..150670376-chr1:150778150..150781017,2	K562	blood:
3	chr1:150533891..150536249-chr1:150780759..150782445,2	MCF-7	breast:
4	chr1:150720934..150724836-chr1:150780473..150783915,3	K562	blood:

No data

Variant related genes	Relation type
CTSK	TF binding region
ENSG00000143457	Chromatin interaction
ENSG00000163131	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000203804	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11799727	1.00[AMR][1000 genomes]
rs11809393	1.00[AMR][1000 genomes]
rs12065659	1.00[AMR][1000 genomes]
rs12075189	1.00[AMR][1000 genomes]
rs12088369	1.00[AMR][1000 genomes]
rs12092817	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12093938	1.00[AMR][1000 genomes]
rs16839661	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs35822171	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv2788	chr1:150755334-150800785	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150761200-150783200	Weak transcription	GM12878-XiMat	blood
2	chr1:150764600-150781600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:150765400-150781400	Weak transcription	HMEC	breast
4	chr1:150765400-150793600	Weak transcription	Fetal Heart	heart
5	chr1:150767600-150783600	Weak transcription	Psoas Muscle	Psoas
6	chr1:150768200-150784000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:150769400-150785200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:150770000-150781600	Weak transcription	HSMMtube	muscle
9	chr1:150770400-150783400	Weak transcription	Stomach Mucosa	stomach
10	chr1:150770600-150783600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:150771200-150784600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:150771200-150785400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:150771400-150783000	Weak transcription	Brain Germinal Matrix	brain
14	chr1:150771600-150785200	Weak transcription	Pancreas	Pancrea
15	chr1:150771800-150783600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:150771800-150783600	Weak transcription	A549	lung
17	chr1:150772200-150782200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:150772200-150782200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:150772200-150782400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:150772200-150782400	Weak transcription	Lung	lung
21	chr1:150772200-150783200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:150772200-150783200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:150772200-150783200	Weak transcription	Spleen	Spleen
24	chr1:150772400-150782800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:150772400-150783600	Weak transcription	Right Ventricle	heart
26	chr1:150772600-150785200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:150773000-150783400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:150773200-150782200	Weak transcription	NH-A	brain
29	chr1:150773600-150782200	Weak transcription	HSMM	muscle
30	chr1:150775800-150784600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:150776200-150782800	Weak transcription	K562	blood
32	chr1:150776800-150781200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:150776800-150783400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:150777000-150781600	Weak transcription	Placenta	Placenta
35	chr1:150777000-150782200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:150777800-150784600	Weak transcription	Hela-S3	cervix
37	chr1:150778200-150781000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:150778200-150781000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr1:150778400-150781000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:150778400-150781400	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:150778400-150781400	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr1:150779000-150781000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:150779000-150781200	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr1:150779000-150781600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:150779200-150781000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr1:150779200-150781000	Active TSS	Duodenum Mucosa	Duodenum
47	chr1:150779200-150781000	Active TSS	Fetal Stomach	stomach
48	chr1:150779200-150781200	Active TSS	Rectal Smooth Muscle	rectum
49	chr1:150779200-150781200	Active TSS	Stomach Smooth Muscle	stomach
50	chr1:150779200-150781400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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