Variant report

Variant	rs7550857
Chromosome Location	chr1:209956542-209956543
allele	A/C
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	chr1:209955222..209959394-chr1:210545816..210547914,4	K562	blood:
2	chr1:209940844..209943415-chr1:209955888..209958090,3	K562	blood:
3	chr1:209946631..209949857-chr1:209956266..209959109,3	MCF-7	breast:
4	chr1:209947385..209948947-chr1:209955247..209957526,2	MCF-7	breast:
5	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
6	chr1:209955222..209958022-chr1:210545930..210547914,2	K562	blood:
7	chr1:209802370..209804993-chr1:209955747..209957464,2	K562	blood:
8	chr1:209954505..209956563-chr1:209958183..209960148,2	K562	blood:
9	chr1:209950429..209953463-chr1:209956092..209959569,7	K562	blood:
10	chr1:209956517..209958141-chr1:209999783..210001469,2	MCF-7	breast:
11	chr1:209953015..209954990-chr1:209956352..209958315,2	MCF-7	breast:
12	chr1:209955602..209959674-chr1:209962858..209967873,6	MCF-7	breast:
13	chr1:209956289..209959543-chr1:209978892..209981541,4	K562	blood:
14	chr1:209921622..209924785-chr1:209954989..209957828,3	MCF-7	breast:
15	chr1:209935010..209937588-chr1:209955355..209957792,2	K562	blood:
16	chr1:209954399..209956563-chr1:209957596..209960148,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117595	Chromatin interaction
ENSG00000009790	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000117597	Chromatin interaction
ENSG00000162757	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1044516	0.86[ASW][hapmap];0.83[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1073150	0.83[ASN][1000 genomes]
rs11803382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11805830	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12070337	0.87[AFR][1000 genomes]
rs12403599	0.95[YRI][hapmap]
rs1319072	0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs1415543	0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs17015183	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17015218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015224	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015259	0.87[EUR][1000 genomes]
rs17015309	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs17015330	0.90[ASN][1000 genomes]
rs17015361	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17015379	0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs17317411	1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2013162	0.86[LWK][hapmap];0.95[YRI][hapmap]
rs2073485	0.93[ASW][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2073486	0.86[LWK][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs2073487	0.95[YRI][hapmap]
rs2235372	0.86[ASW][hapmap];0.83[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2235373	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2235375	0.82[LWK][hapmap];0.95[YRI][hapmap]
rs2236908	0.86[LWK][hapmap];0.95[YRI][hapmap]
rs2236909	0.86[LWK][hapmap];0.95[YRI][hapmap]
rs2357229	0.94[YRI][hapmap]
rs2357230	0.88[ASN][1000 genomes]
rs3753518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41305104	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4556361	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs4844895	0.86[ASW][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs58637469	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59100111	0.88[ASN][1000 genomes]
rs61747285	0.90[ASN][1000 genomes]
rs6540559	0.87[EUR][1000 genomes]
rs6540560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540561	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540563	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6540564	0.88[ASN][1000 genomes]
rs6685182	0.86[LWK][hapmap];0.95[YRI][hapmap]
rs6694552	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696825	0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs6698154	0.90[ASN][1000 genomes]
rs73093853	0.83[ASN][1000 genomes]
rs742214	0.87[EUR][1000 genomes]
rs742215	0.80[ASW][hapmap];0.80[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7511996	0.83[ASN][1000 genomes]
rs7522045	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7522250	0.87[EUR][1000 genomes]
rs7525951	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs7539638	0.90[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs7545542	0.90[LWK][hapmap];0.95[YRI][hapmap]
rs7552506	0.90[LWK][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs764093	0.87[EUR][1000 genomes]
rs926346	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926347	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS 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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1067914	chr1:209955818-209972979	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7550857	TRAF3IP3	cis	Whole Blood	GTEx
rs7550857	LAMB3	cis	parietal	SCAN
rs7550857	DYRK3	cis	parietal	SCAN
rs7550857	SYT14	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209942800-209956800	Weak transcription	Small Intestine	intestine
2	chr1:209942800-209957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:209943600-209956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:209943800-209956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:209943800-209956600	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:209943800-209957000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:209943800-209957200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:209944000-209956600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:209944800-209956600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:209944800-209956600	Weak transcription	Right Ventricle	heart
11	chr1:209945000-209956600	Weak transcription	Adipose Nuclei	Adipose
12	chr1:209945000-209956600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:209945000-209956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:209945000-209956600	Weak transcription	Esophagus	oesophagus
15	chr1:209945000-209956600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:209945000-209956800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:209945000-209956800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:209945200-209956600	Weak transcription	Colonic Mucosa	Colon
19	chr1:209945200-209956600	Weak transcription	Pancreas	Pancrea
20	chr1:209945200-209957200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:209945600-209956600	Weak transcription	Fetal Lung	lung
22	chr1:209945800-209956600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:209946000-209956600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:209946000-209956600	Strong transcription	Fetal Thymus	thymus
25	chr1:209946200-209956600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:209946400-209956800	Strong transcription	Primary hematopoietic stem cells	blood
27	chr1:209947600-209956600	Strong transcription	Thymus	Thymus
28	chr1:209949200-209956600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr1:209949200-209957000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:209949800-209956600	Strong transcription	Primary B cells from cord blood	blood
31	chr1:209950000-209956600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:209950000-209956800	Strong transcription	Primary T cells from cord blood	blood
33	chr1:209950200-209957400	Weak transcription	Aorta	Aorta
34	chr1:209951400-209956600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:209951400-209956600	Weak transcription	HSMM	muscle
36	chr1:209951600-209956600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:209951600-209956600	Weak transcription	Psoas Muscle	Psoas
38	chr1:209951600-209956800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:209951800-209956600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:209952000-209957000	Weak transcription	HUVEC	blood vessel
41	chr1:209952200-209956600	Weak transcription	NHLF	lung
42	chr1:209952800-209956800	Strong transcription	HMEC	breast
43	chr1:209953400-209956600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:209953400-209956600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:209953800-209956600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:209953800-209956800	Weak transcription	Stomach Mucosa	stomach
47	chr1:209953800-209957400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr1:209954000-209956600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:209954000-209956600	Weak transcription	Liver	Liver
50	chr1:209954200-209956800	Weak transcription	Placenta	Placenta

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