Variant report

Variant	rs4747994
Chromosome Location	chr10:6342636-6342637
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:6243246..6245035-chr10:6341115..6343745,2	K562	blood:
2	chr10:6240895..6249179-chr10:6337425..6345825,48	MCF-7	breast:
3	chr10:6249507..6251896-chr10:6339799..6342783,2	MCF-7	breast:
4	chr10:6341160..6345288-chr10:6356730..6359741,4	MCF-7	breast:
5	chr10:6242967..6247217-chr10:6336875..6343685,22	MCF-7	breast:
6	chr10:6338687..6345306-chr10:6353335..6358938,10	MCF-7	breast:
7	chr10:6316454..6323166-chr10:6337458..6343783,14	MCF-7	breast:
8	chr10:6339849..6343647-chr10:6369137..6372590,4	MCF-7	breast:
9	chr10:6338433..6344348-chr10:6402915..6408706,10	MCF-7	breast:
10	chr10:6342449..6344753-chr10:6350540..6352238,2	K562	blood:
11	chr10:6148853..6150588-chr10:6340669..6343232,2	MCF-7	breast:
12	chr10:6339437..6341250-chr10:6341763..6343524,3	MCF-7	breast:
13	chr10:6339999..6343004-chr10:6366040..6368957,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213994	Chromatin interaction
ENSG00000170525	Chromatin interaction
ENSG00000215244	Chromatin interaction
ENSG00000134453	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10906207	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11257854	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12259346	0.96[ASN][1000 genomes]
rs4403713	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4420170	0.84[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6602609	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7088356	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7896262	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7906792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7907381	0.84[CEU][hapmap]
rs7918684	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7921642	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1041039	chr10:6217724-6354858	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats 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 target site	19 gene(s)	inside rSNPs	diseases
5	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription 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	13 gene(s)	inside rSNPs	diseases
7	nsv971867	chr10:6341441-6353045	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4747994	IL2RA	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6338400-6344000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr10:6338600-6343000	Enhancers	HMEC	breast
3	chr10:6338600-6343800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr10:6338800-6342800	Enhancers	Aorta	Aorta
5	chr10:6338800-6343800	Enhancers	Stomach Mucosa	stomach
6	chr10:6338800-6345000	Enhancers	Fetal Intestine Small	intestine
7	chr10:6339000-6343800	Enhancers	Lung	lung
8	chr10:6339200-6345200	Enhancers	Fetal Intestine Large	intestine
9	chr10:6339400-6342800	Weak transcription	Spleen	Spleen
10	chr10:6339600-6343800	Enhancers	Primary B cells from peripheral blood	blood
11	chr10:6339600-6346400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr10:6339800-6342800	Enhancers	Brain Substantia Nigra	brain
13	chr10:6339800-6343000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:6340200-6343400	Weak transcription	Fetal Kidney	kidney
15	chr10:6340200-6349000	Weak transcription	Adipose Nuclei	Adipose
16	chr10:6340600-6343200	Enhancers	Brain Anterior Caudate	brain
17	chr10:6340800-6342800	Weak transcription	Brain Hippocampus Middle	brain
18	chr10:6340800-6343000	Enhancers	Gastric	stomach
19	chr10:6341200-6343200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr10:6341200-6343200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:6341200-6343400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr10:6341400-6342800	Enhancers	Placenta	Placenta
23	chr10:6341600-6342800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr10:6341600-6342800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr10:6341600-6343000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr10:6341600-6343000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr10:6341600-6343000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr10:6341600-6343000	Enhancers	Fetal Thymus	thymus
29	chr10:6341600-6343000	Enhancers	Small Intestine	intestine
30	chr10:6341600-6343200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr10:6341600-6343200	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr10:6341600-6343200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr10:6341600-6343400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr10:6341800-6342800	Weak transcription	Pancreas	Pancrea
35	chr10:6341800-6343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:6341800-6343200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr10:6341800-6343800	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr10:6341800-6344200	Enhancers	A549	lung
39	chr10:6342000-6342800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr10:6342000-6343000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr10:6342000-6343000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr10:6342000-6343200	Flanking Active TSS	Dnd41	blood
43	chr10:6342000-6343800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:6342000-6343800	Enhancers	Fetal Lung	lung
45	chr10:6342200-6342800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr10:6342200-6342800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr10:6342200-6342800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr10:6342200-6342800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr10:6342200-6342800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr10:6342200-6342800	Active TSS	Rectal Mucosa Donor 29	rectum

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