Variant report

Variant	rs12093044
Chromosome Location	chr1:228318997-228318998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227669108..227669644-chr1:228318559..228319309,2	K562	blood:
2	chr1:228296587..228298134-chr1:228317417..228319245,2	MCF-7	breast:
3	chr1:228318245..228320803-chr1:228645102..228647323,2	MCF-7	breast:
4	chr1:228296837..228298966-chr1:228317403..228319200,2	MCF-7	breast:
5	chr1:228318444..228319355-chr1:228580810..228581597,3	MCF-7	breast:
6	chr1:228317307..228320244-chr1:228593254..228595071,2	MCF-7	breast:
7	chr1:228318795..228319443-chr1:228326879..228327649,2	K562	blood:
8	chr1:228318704..228321290-chr1:228321763..228325598,5	K562	blood:
9	chr1:228317360..228320048-chr1:228643318..228645698,2	K562	blood:
10	chr1:228318929..228320928-chr1:228352510..228356054,3	MCF-7	breast:
11	chr1:228318400..228319358-chr1:228379072..228379959,2	MCF-7	breast:
12	chr1:228318237..228319764-chr1:228400846..228402736,2	K562	blood:
13	chr1:228318799..228319507-chr1:228353439..228354347,2	K562	blood:
14	chr1:228191780..228193444-chr1:228317568..228320348,2	MCF-7	breast:
15	chr1:228318736..228319366-chr1:228328855..228329758,2	K562	blood:
16	chr1:228317576..228320625-chr1:228326165..228329627,4	MCF-7	breast:
17	chr1:228308851..228311913-chr1:228318385..228321498,4	K562	blood:
18	chr1:228317547..228320565-chr1:228350763..228355962,5	MCF-7	breast:
19	chr1:228261534..228262217-chr1:228318541..228319233,2	MCF-7	breast:
20	chr1:228318319..228319575-chr1:228353004..228354801,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162910	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000227625	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000162913	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000196890	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11804099	1.00[EUR][1000 genomes]
rs11809443	0.84[LWK][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs12090413	1.00[EUR][1000 genomes]
rs12092786	1.00[EUR][1000 genomes]
rs12095133	1.00[EUR][1000 genomes]
rs2313121	1.00[EUR][1000 genomes]
rs287606	0.81[YRI][hapmap]
rs397637	0.81[YRI][hapmap]
rs424645	0.81[YRI][hapmap]
rs4396117	1.00[EUR][1000 genomes]
rs549590	0.81[YRI][hapmap]
rs6701173	0.80[YRI][hapmap]
rs74140903	1.00[EUR][1000 genomes]
rs74142661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74142677	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
5	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
9	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription 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 miRNA target site	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228318000-228319200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:228318200-228319000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:228318200-228319000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:228318200-228319000	Active TSS	A549	lung
5	chr1:228318200-228319000	Bivalent Enhancer	Osteobl	bone
6	chr1:228318200-228319200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:228318200-228319200	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:228318200-228319400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:228318200-228319800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:228318200-228319800	Enhancers	Fetal Intestine Large	intestine
11	chr1:228318200-228319800	Enhancers	Placenta	Placenta
12	chr1:228318200-228319800	Enhancers	HMEC	breast
13	chr1:228318400-228319000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:228318400-228319000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:228318400-228319000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:228318400-228319200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:228318400-228319200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr1:228318400-228319200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:228318600-228319000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:228318600-228319000	Active TSS	Primary T cells from cord blood	blood
21	chr1:228318600-228319000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr1:228318600-228319000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:228318600-228319000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:228318600-228319000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:228318600-228319000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:228318600-228319000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:228318600-228319000	Active TSS	Brain Angular Gyrus	brain
28	chr1:228318600-228319000	Active TSS	Brain Anterior Caudate	brain
29	chr1:228318600-228319000	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:228318600-228319000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:228318600-228319000	Active TSS	Rectal Smooth Muscle	rectum
32	chr1:228318600-228319000	Enhancers	Dnd41	blood
33	chr1:228318600-228319200	Enhancers	Fetal Lung	lung
34	chr1:228318600-228319200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr1:228318600-228319600	Enhancers	Hela-S3	cervix
36	chr1:228318800-228319000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:228318800-228319000	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr1:228318800-228319000	Active TSS	Primary B cells from cord blood	blood
39	chr1:228318800-228319000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:228318800-228319000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:228318800-228319000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:228318800-228319000	Active TSS	Monocytes-CD14+_RO01746	blood
43	chr1:228318800-228319200	Flanking Active TSS	Fetal Kidney	kidney
44	chr1:228318800-228319200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:228318800-228319200	Enhancers	K562	blood
46	chr1:228318800-228319400	Enhancers	HepG2	liver
47	chr1:228318800-228319400	Flanking Active TSS	NHEK	skin
48	chr1:228318800-228319600	Enhancers	Stomach Mucosa	stomach
49	chr1:228318800-228319800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:228318800-228319800	Enhancers	Fetal Intestine Small	intestine

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