Variant report

Variant	rs2705554
Chromosome Location	chr3:112273546-112273547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112271839..112274196-chr3:112276069..112278465,2	K562	blood:
2	chr3:112270877..112274678-chr3:112278992..112281610,4	MCF-7	breast:
3	chr3:112272044..112274714-chr3:112358450..112360286,2	MCF-7	breast:
4	chr3:112267834..112269856-chr3:112273355..112275580,2	MCF-7	breast:
5	chr3:112272255..112274870-chr3:112277581..112280165,3	K562	blood:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10934177	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386896	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1388442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472106	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488260	1.00[ASN][1000 genomes]
rs1488262	1.00[ASN][1000 genomes]
rs1491629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532198	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814053	1.00[ASN][1000 genomes]
rs1817694	1.00[ASN][1000 genomes]
rs1844864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877364	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906519	1.00[ASN][1000 genomes]
rs2029317	1.00[ASN][1000 genomes]
rs2399431	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464612	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638025	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638030	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638033	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638036	1.00[ASN][1000 genomes]
rs2638038	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2638041	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638043	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2638044	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668216	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2705510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705520	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705524	1.00[ASN][1000 genomes]
rs2705551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2931761	1.00[ASW][hapmap]
rs2933139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969894	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109033	0.86[ASN][1000 genomes]
rs62264580	0.83[ASN][1000 genomes]
rs6793232	1.00[ASN][1000 genomes]
rs7612851	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7618978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901829	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs971832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active 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 target site	28 gene(s)	inside rSNPs	diseases
6	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers 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	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2705554	GUCA1C	trans	brain	seeQTL
rs2705554	LRTM1	trans	brain	seeQTL
rs2705554	SH2D2A	trans	brain	seeQTL
rs2705554	CRX	trans	brain	seeQTL
rs2705554	SLC5A7	trans	brain	seeQTL
rs2705554	TTR	trans	brain	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112244400-112274200	Weak transcription	Stomach Mucosa	stomach
2	chr3:112244400-112278200	Weak transcription	K562	blood
3	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
4	chr3:112245800-112279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:112247600-112279600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:112248400-112274200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:112249200-112275800	Weak transcription	Fetal Stomach	stomach
8	chr3:112249200-112276000	Weak transcription	Spleen	Spleen
9	chr3:112249200-112278200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:112249200-112278400	Weak transcription	Aorta	Aorta
11	chr3:112249200-112279600	Weak transcription	Esophagus	oesophagus
12	chr3:112249200-112279600	Weak transcription	Gastric	stomach
13	chr3:112249200-112279800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:112249400-112276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:112249400-112279600	Weak transcription	Lung	lung
16	chr3:112251000-112274200	Weak transcription	Brain Angular Gyrus	brain
17	chr3:112252600-112278400	Weak transcription	Fetal Kidney	kidney
18	chr3:112253200-112278600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:112254200-112273600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:112257600-112274000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:112260000-112278200	Weak transcription	Fetal Brain Male	brain
22	chr3:112260400-112279600	Weak transcription	Pancreas	Pancrea
23	chr3:112265000-112276000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:112266000-112274200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:112266200-112278200	Weak transcription	Fetal Heart	heart
26	chr3:112266200-112278200	Weak transcription	NHLF	lung
27	chr3:112266200-112278400	Weak transcription	Colonic Mucosa	Colon
28	chr3:112266400-112278200	Weak transcription	NHEK	skin
29	chr3:112266800-112274400	Weak transcription	A549	lung
30	chr3:112266800-112278400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:112267000-112274000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:112267000-112274000	Weak transcription	HUVEC	blood vessel
33	chr3:112267000-112274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:112267000-112278400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:112267000-112278400	Weak transcription	NHDF-Ad	bronchial
36	chr3:112267200-112274200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:112267200-112276000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:112267200-112276000	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:112267200-112278400	Weak transcription	Thymus	Thymus
40	chr3:112267200-112279200	Weak transcription	Right Ventricle	heart
41	chr3:112267400-112274400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:112267600-112274800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:112267600-112275800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:112267600-112278200	Weak transcription	Ovary	ovary
45	chr3:112267600-112278600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:112267600-112279600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:112267800-112274000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:112267800-112274400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:112267800-112274400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:112267800-112275800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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