Variant report

Variant	rs11801489
Chromosome Location	chr1:76189315-76189316
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	chr1:76189138-76190794	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:76188834-76190820	K562	blood:	n/a	n/a
3	MYC	chr1:76188822-76190918	K562	blood:	n/a	chr1:76190102-76190112
4	TBP	chr1:76189244-76190760	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:76189169-76190755	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr1:76188970-76190848	HepG2	liver:	n/a	n/a
7	RCOR1	chr1:76189250-76190827	K562	blood:	n/a	n/a
8	MYC	chr1:76188955-76190842	K562	blood:	n/a	chr1:76190102-76190112
9	KAP1	chr1:76188675-76189667	K562	blood:	n/a	n/a
10	POLR2A	chr1:76189108-76189426	K562	blood:	n/a	n/a
11	POLR2A	chr1:76188739-76192883	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:76189286-76190972	HUVEC	blood vessel:	n/a	n/a
13	HEY1	chr1:76188988-76190854	K562	blood:	n/a	n/a
14	HCFC1	chr1:76189167-76190944	Hela-S3	cervix:	n/a	n/a
15	IRF1	chr1:76189245-76193364	K562	blood:	n/a	chr1:76189864-76189877 chr1:76190686-76190700 chr1:76190686-76190696 chr1:76192789-76192803 chr1:76190682-76190696 chr1:76192789-76192800 chr1:76190680-76190697 chr1:76190381-76190395 chr1:76189864-76189878 chr1:76189864-76189876 chr1:76190001-76190015 chr1:76190685-76190696 chr1:76192789-76192802 chr1:76190176-76190187 chr1:76193209-76193221 chr1:76192989-76193000 chr1:76192790-76192800 chr1:76189863-76189874 chr1:76189864-76189877 chr1:76191327-76191339 chr1:76192789-76192802 chr1:76192790-76192804 chr1:76192989-76193003 chr1:76190684-76190704 chr1:76192789-76192802 chr1:76189859-76189876
16	NR2F2	chr1:76189259-76190748	K562	blood:	n/a	chr1:76189800-76189815 chr1:76190250-76190265 chr1:76189566-76189581
17	ZMIZ1	chr1:76189185-76190703	K562	blood:	n/a	n/a
18	POLR2A	chr1:76188877-76191606	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:76188418-76192901	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:76188832-76190830	K562	blood:	n/a	n/a
21	USF2	chr1:76189280-76189976	Hela-S3	cervix:	n/a	n/a
22	IRF1	chr1:76189162-76192393	K562	blood:	n/a	chr1:76189864-76189877 chr1:76190686-76190700 chr1:76190686-76190696 chr1:76190682-76190696 chr1:76190680-76190697 chr1:76190381-76190395 chr1:76189864-76189878 chr1:76189864-76189876 chr1:76190001-76190015 chr1:76190685-76190696 chr1:76190176-76190187 chr1:76189863-76189874 chr1:76189864-76189877 chr1:76191327-76191339 chr1:76190684-76190704 chr1:76189859-76189876
23	TBL1XR1	chr1:76189086-76189392	K562	blood:	n/a	n/a
24	POLR2A	chr1:76188459-76189326	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr1:76188727-76189345	K562	blood:	n/a	n/a
26	MXI1	chr1:76189073-76192452	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr1:76188161-76190823	Raji	blood:	n/a	n/a
28	POLR2A	chr1:76189176-76190696	K562	blood:	n/a	n/a
29	BRCA1	chr1:76189124-76190021	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:76189223-76190909	HepG2	liver:	n/a	n/a
31	MYC	chr1:76188943-76191174	K562	blood:	n/a	chr1:76190102-76190112
32	UBTF	chr1:76189276-76192340	K562	blood:	n/a	n/a
33	POLR2A	chr1:76189160-76190831	K562	blood:	n/a	n/a
34	MXI1	chr1:76189277-76191416	IMR90	lung:	n/a	n/a
35	POLR2A	chr1:76189166-76191021	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr1:76188052-76192437	K562	blood:	n/a	n/a
37	POLR2A	chr1:76189072-76190927	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:76187324..76189486-chr1:76251695..76253876,2	MCF-7	breast:
2	chr1:76188769..76191418-chr1:76197121..76200007,3	MCF-7	breast:
3	chr1:76188658..76192178-chr1:76249968..76253902,5	MCF-7	breast:
4	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
5	chr1:76188740..76191486-chr1:76199573..76201902,4	K562	blood:
6	chr1:76188764..76194417-chr1:76259356..76264333,14	K562	blood:
7	chr1:76189028..76194220-chr1:76209012..76215464,6	K562	blood:
8	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:

Variant related genes	Relation type
ACADM	TF binding region
ENSG00000137955	Chromatin interaction
ENSG00000201487	Chromatin interaction
ENSG00000181227	Chromatin interaction
ENSG00000057468	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000207241	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11799338	1.00[EUR][1000 genomes]
rs11803595	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11803965	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11803967	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11806876	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11809577	0.86[AFR][1000 genomes]
rs11809592	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11810780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11811276	0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11811907	0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs5745467	0.91[YRI][hapmap]
rs961362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv870520	chr1:76088392-76206490	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv871572	chr1:76161889-76208488	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76186000-76189600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:76186800-76189400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:76187200-76189400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:76187200-76189400	Weak transcription	Fetal Thymus	thymus
5	chr1:76187200-76189600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:76187400-76189400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:76187600-76189400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:76188200-76189600	Flanking Active TSS	NHEK	skin
9	chr1:76188400-76189400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:76188400-76189600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:76188800-76189400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:76189000-76189400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:76189000-76189400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:76189000-76189400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr1:76189000-76189400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:76189000-76189400	Enhancers	Gastric	stomach
17	chr1:76189000-76189400	Enhancers	Ovary	ovary
18	chr1:76189000-76189400	Enhancers	Psoas Muscle	Psoas
19	chr1:76189000-76189400	Enhancers	Right Atrium	heart
20	chr1:76189000-76189400	Enhancers	Spleen	Spleen
21	chr1:76189000-76189400	Flanking Active TSS	K562	blood
22	chr1:76189000-76189600	Enhancers	Primary T cells from cord blood	blood
23	chr1:76189000-76189600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:76189000-76189600	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr1:76189000-76189800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:76189000-76189800	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr1:76189000-76189800	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr1:76189000-76191200	Active TSS	Brain Hippocampus Middle	brain
29	chr1:76189000-76191400	Active TSS	A549	lung
30	chr1:76189000-76191600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:76189000-76191600	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr1:76189200-76189400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr1:76189200-76189400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:76189200-76189400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr1:76189200-76189400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:76189200-76189400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:76189200-76189400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:76189200-76189400	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:76189200-76189400	Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr1:76189200-76189400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr1:76189200-76189400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr1:76189200-76189400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:76189200-76189400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:76189200-76189400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:76189200-76189400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:76189200-76189400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:76189200-76189400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:76189200-76189400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:76189200-76189400	Enhancers	Adipose Nuclei	Adipose
50	chr1:76189200-76189400	Flanking Active TSS	Brain Germinal Matrix	brain

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