Variant report

Variant	rs1798172
Chromosome Location	chr11:57430136-57430137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57429911..57430515-chr11:57567834..57568398,2	MCF-7	breast:
2	chr11:57427400..57431333-chr11:57432768..57435307,4	MCF-7	breast:
3	chr11:57423642..57427041-chr11:57427345..57431533,5	K562	blood:
4	chr11:57423095..57430151-chr11:57432283..57438412,24	K562	blood:
5	chr11:57427698..57431931-chr11:57435517..57438480,4	MCF-7	breast:
6	chr11:57429293..57431231-chr11:57440462..57442351,2	K562	blood:
7	chr11:57427688..57430465-chr11:57507788..57510350,2	K562	blood:

Variant related genes	Relation type
ENSG00000172409	Chromatin interaction
ENSG00000156599	Chromatin interaction
ENSG00000254732	Chromatin interaction
ENSG00000211450	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10750870	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs10792110	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10896644	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs10896649	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10896653	0.82[ASN][1000 genomes]
rs11229109	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11570176	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs11570181	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs12270209	0.84[ASN][1000 genomes]
rs12274865	0.84[ASN][1000 genomes]
rs12363024	0.85[ASN][1000 genomes]
rs12805343	0.82[ASN][1000 genomes]
rs1424753	0.85[ASN][1000 genomes]
rs1613592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1624389	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1631684	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1647394	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1647403	0.82[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455422	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs17455626	0.85[ASN][1000 genomes]
rs1783818	0.85[CEU][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1783824	0.82[ASN][1000 genomes]
rs1783826	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1783827	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1783828	0.84[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1783829	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1783976	0.85[ASN][1000 genomes]
rs1783978	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs1783979	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs1783980	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1783981	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1783983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1783984	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1783985	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1785498	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1785499	0.82[ASN][1000 genomes]
rs1798173	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798177	0.84[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2156638	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2956981	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs2956982	0.82[ASN][1000 genomes]
rs3017889	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs36036499	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs4611222	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs56392705	0.82[ASN][1000 genomes]
rs627145	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs644219	0.82[ASN][1000 genomes]
rs645145	0.82[ASN][1000 genomes]
rs652191	0.82[ASN][1000 genomes]
rs653889	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs659165	0.82[ASN][1000 genomes]
rs665058	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs671508	0.82[ASN][1000 genomes]
rs682258	0.82[ASN][1000 genomes]
rs686489	0.83[ASN][1000 genomes]
rs7105506	0.85[ASN][1000 genomes]
rs7115528	0.85[ASN][1000 genomes]
rs7117020	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs7120868	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs7479922	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7947357	0.84[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs929934	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers 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 miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1798172	SLC43A3	cis	cerebellum	SCAN
rs1798172	MS4A7	cis	parietal	SCAN
rs1798172	YPEL4	cis	lung	GTEx
rs1798172	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs1798172	OR4C11	cis	cerebellum	SCAN
rs1798172	TIMM10	cis	parietal	SCAN
rs1798172	YPEL4	cis	lymphoblastoid	seeQTL
rs1798172	TNKS1BP1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57426000-57434000	Weak transcription	Fetal Heart	heart
2	chr11:57426000-57434000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:57426000-57434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:57426000-57434200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:57426400-57430600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:57426400-57431400	Strong transcription	Fetal Stomach	stomach
7	chr11:57426600-57430600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:57426600-57430600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr11:57426800-57430200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr11:57426800-57430200	Strong transcription	K562	blood
11	chr11:57426800-57430400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:57426800-57430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:57426800-57430600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:57426800-57430600	Strong transcription	Adipose Nuclei	Adipose
15	chr11:57426800-57430600	Strong transcription	Fetal Intestine Large	intestine
16	chr11:57426800-57430600	Strong transcription	Placenta	Placenta
17	chr11:57426800-57430600	Strong transcription	HSMM	muscle
18	chr11:57426800-57430800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr11:57426800-57430800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:57426800-57430800	Strong transcription	Fetal Muscle Leg	muscle
21	chr11:57426800-57430800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr11:57427000-57430200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:57427000-57430200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:57427000-57430200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:57427000-57430200	Strong transcription	Primary hematopoietic stem cells	blood
26	chr11:57427000-57430200	Strong transcription	Brain Angular Gyrus	brain
27	chr11:57427000-57430200	Strong transcription	Fetal Lung	lung
28	chr11:57427000-57430200	Strong transcription	HSMMtube	muscle
29	chr11:57427000-57430400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:57427000-57430400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:57427000-57430400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:57427000-57430400	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:57427000-57430400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:57427000-57430400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:57427000-57430400	Strong transcription	Brain Hippocampus Middle	brain
36	chr11:57427000-57430400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr11:57427000-57430400	Strong transcription	Rectal Smooth Muscle	rectum
38	chr11:57427000-57430400	Strong transcription	HUVEC	blood vessel
39	chr11:57427000-57430600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:57427000-57430600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:57427000-57430600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:57427000-57430600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:57427000-57430600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr11:57427000-57430600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:57427000-57430600	Strong transcription	Liver	Liver
46	chr11:57427000-57430600	Strong transcription	Brain Anterior Caudate	brain
47	chr11:57427000-57430600	Strong transcription	Brain Cingulate Gyrus	brain
48	chr11:57427000-57430600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr11:57427000-57430600	Strong transcription	Fetal Thymus	thymus
50	chr11:57427000-57430600	Strong transcription	Rectal Mucosa Donor 31	rectum

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