Variant report

Variant	rs1289473
Chromosome Location	chr1:227129720-227129721
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227129578..227135154-chr1:227160579..227165321,6	K562	blood:
2	chr1:227127948..227129868-chr1:227162930..227165927,2	MCF-7	breast:
3	chr1:227129122..227132019-chr1:227132430..227134226,2	MCF-7	breast:
4	chr1:227127006..227129793-chr1:227152681..227157136,4	K562	blood:
5	chr1:227125746..227127368-chr1:227129287..227131085,2	MCF-7	breast:
6	chr1:227129636..227132325-chr1:227181300..227183713,2	K562	blood:
7	chr1:227058010..227060717-chr1:227127922..227130467,2	K562	blood:
8	chr1:227128683..227130385-chr1:227174300..227176049,2	MCF-7	breast:
9	chr1:227129304..227131078-chr1:227159225..227162079,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10482	1.00[GIH][hapmap]
rs2802273	0.85[CEU][hapmap]
rs2802274	0.85[CEU][hapmap]
rs4653781	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv873236	chr1:227118912-227173537	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
6	nsv549268	chr1:227124660-227149203	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
7	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1289473	SGCE	trans	lymphoblastoid	seeQTL
rs1289473	ADCK3	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227126400-227130000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:227128000-227130400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr1:227128000-227131200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:227128600-227131800	Enhancers	HSMMtube	muscle
5	chr1:227128600-227136600	Weak transcription	Aorta	Aorta
6	chr1:227128800-227130000	Enhancers	Placenta	Placenta
7	chr1:227128800-227130200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:227128800-227130200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:227128800-227130400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:227128800-227130400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:227128800-227130400	Flanking Active TSS	HepG2	liver
12	chr1:227128800-227132000	Enhancers	Small Intestine	intestine
13	chr1:227128800-227132800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:227128800-227133000	Weak transcription	HSMM	muscle
15	chr1:227128800-227135400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:227129000-227129800	Active TSS	Right Ventricle	heart
17	chr1:227129000-227130000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:227129000-227130000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:227129000-227130200	Genic enhancers	Fetal Intestine Small	intestine
20	chr1:227129000-227130200	Enhancers	Lung	lung
21	chr1:227129000-227130400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:227129000-227130400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:227129000-227130400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:227129000-227130400	Enhancers	Fetal Thymus	thymus
25	chr1:227129000-227130600	Weak transcription	Osteobl	bone
26	chr1:227129000-227130800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:227129000-227131000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr1:227129000-227131400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr1:227129000-227131400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:227129000-227131600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:227129000-227131600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:227129000-227131800	Enhancers	Primary B cells from peripheral blood	blood
33	chr1:227129000-227132600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:227129000-227132600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:227129000-227132800	Weak transcription	Fetal Lung	lung
36	chr1:227129000-227132800	Weak transcription	A549	lung
37	chr1:227129000-227133400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:227129000-227133600	Enhancers	Spleen	Spleen
39	chr1:227129000-227134400	Enhancers	Fetal Intestine Large	intestine
40	chr1:227129000-227134400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr1:227129000-227134400	Weak transcription	NHDF-Ad	bronchial
42	chr1:227129000-227134800	Weak transcription	Fetal Brain Female	brain
43	chr1:227129000-227135000	Enhancers	Fetal Muscle Leg	muscle
44	chr1:227129000-227162600	Weak transcription	Fetal Kidney	kidney
45	chr1:227129200-227129800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:227129200-227129800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:227129200-227129800	Enhancers	Brain Cingulate Gyrus	brain
48	chr1:227129200-227129800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr1:227129200-227129800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:227129200-227129800	Active TSS	Duodenum Smooth Muscle	Duodenum

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