Variant report

Variant	rs622623
Chromosome Location	chr1:10555257-10555258
allele	C/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10269919..10270914-chr1:10554482..10555369,2	K562	blood:
2	chr1:10488833..10492668-chr1:10552829..10556296,4	MCF-7	breast:
3	chr1:10437389..10440210-chr1:10554525..10556492,2	K562	blood:
4	chr1:10490211..10490965-chr1:10554619..10555366,4	MCF-7	breast:
5	chr1:10543950..10546722-chr1:10553163..10555710,2	K562	blood:
6	chr1:10530530..10533287-chr1:10554066..10555649,2	K562	blood:
7	chr1:10536268..10539627-chr1:10553457..10556201,3	K562	blood:
8	chr1:10490031..10491039-chr1:10554309..10555652,10	MCF-7	breast:
9	chr1:10554744..10555346-chr1:10567221..10567895,2	MCF-7	breast:
10	chr1:10488234..10492176-chr1:10552870..10556900,4	K562	blood:
11	chr1:10554713..10555456-chr1:10567516..10568024,2	MCF-7	breast:
12	chr1:10489902..10490981-chr1:10554372..10555362,18	K562	blood:
13	chr1:10554756..10555464-chr1:10926875..10927459,2	K562	blood:
14	chr1:10488879..10492501-chr1:10553959..10556720,6	MCF-7	breast:
15	chr1:10533760..10535685-chr1:10553523..10556156,3	MCF-7	breast:
16	chr1:10437203..10438150-chr1:10554425..10555351,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000142655	Chromatin interaction
ENSG00000175279	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000271989	Chromatin interaction
ENSG00000054523	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10864458	0.87[EUR][1000 genomes]
rs10864459	0.95[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs10864460	0.95[CEU][hapmap]
rs11121587	0.82[CHB][hapmap]
rs1152739	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1188525	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1188526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1188528	0.91[EUR][1000 genomes]
rs1188529	0.89[EUR][1000 genomes]
rs12028449	0.95[CHD][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs12375	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs1307489	0.92[CHB][hapmap]
rs1307490	0.84[CHB][hapmap]
rs1307494	0.84[CHB][hapmap]
rs1307497	0.84[CHB][hapmap]
rs1308520	0.92[CHB][hapmap]
rs1411402	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1632108	0.99[EUR][1000 genomes]
rs17035305	0.82[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs2026792	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2056417	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2480777	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs2480782	0.82[CHB][hapmap]
rs2480784	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2480785	0.88[EUR][1000 genomes]
rs2483677	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2483686	0.92[CHB][hapmap]
rs2506880	0.86[EUR][1000 genomes]
rs2506892	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2506896	0.80[EUR][1000 genomes]
rs2506901	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2506902	1.00[CEU][hapmap]
rs2781230	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs2781232	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2847337	0.92[CHB][hapmap]
rs2847344	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs544289	0.84[CHB][hapmap]
rs585870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587916	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs589400	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs596537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597438	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs616402	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs616488	0.91[GIH][hapmap];0.82[TSI][hapmap]
rs617728	0.88[EUR][1000 genomes]
rs620405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636291	0.95[CEU][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs648324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs652771	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6540931	0.90[CHB][hapmap]
rs6540933	0.99[EUR][1000 genomes]
rs657244	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs660725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687430	0.84[CHD][hapmap]
rs668805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs669701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs683864	0.99[EUR][1000 genomes]
rs685746	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs944973	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS 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	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs622623	SLC2A5	cis	parietal	SCAN
rs622623	PLEKHG5	cis	parietal	SCAN
rs622623	AADACL3	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10536000-10555600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:10540600-10555600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:10550400-10556000	Weak transcription	Lung	lung
4	chr1:10553000-10567200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:10553600-10555800	Enhancers	Liver	Liver
6	chr1:10554000-10557000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:10554200-10555600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:10554600-10555400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:10554600-10555600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:10554600-10555600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:10554600-10555600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr1:10554600-10555600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:10554600-10555600	Flanking Active TSS	Dnd41	blood
14	chr1:10554600-10555800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:10554600-10555800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:10554600-10556400	Genic enhancers	Fetal Intestine Small	intestine
17	chr1:10554600-10556600	Enhancers	Fetal Heart	heart
18	chr1:10554600-10556800	Enhancers	Left Ventricle	heart
19	chr1:10554800-10555400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:10554800-10555400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr1:10554800-10555400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:10554800-10555600	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr1:10554800-10555600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr1:10554800-10555600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:10554800-10555600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:10554800-10555600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr1:10554800-10555600	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr1:10554800-10555600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:10554800-10555600	Flanking Active TSS	Fetal Thymus	thymus
30	chr1:10554800-10555600	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr1:10554800-10555600	Genic enhancers	K562	blood
32	chr1:10554800-10555600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr1:10554800-10555600	Flanking Active TSS	Osteobl	bone
34	chr1:10554800-10555800	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr1:10554800-10555800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:10554800-10555800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:10554800-10555800	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr1:10554800-10555800	Enhancers	Placenta	Placenta
39	chr1:10554800-10555800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr1:10554800-10556000	Enhancers	Spleen	Spleen
41	chr1:10554800-10556200	Flanking Active TSS	GM12878-XiMat	blood
42	chr1:10554800-10556400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr1:10554800-10556400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr1:10554800-10556600	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr1:10554800-10556800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr1:10554800-10568600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:10555000-10555400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr1:10555000-10555400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr1:10555000-10555400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr1:10555000-10555400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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