Variant report

Variant	rs1760794
Chromosome Location	chr1:154311696-154311697
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154301040..154304335-chr1:154309259..154312100,3	K562	blood:
2	chr1:154311610..154313113-chr1:154320635..154323090,2	MCF-7	breast:
3	chr1:154303313..154308700-chr1:154311319..154315527,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143515	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10908831	0.96[ASN][1000 genomes]
rs11265604	0.90[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11578607	0.87[EUR][1000 genomes]
rs11581043	0.86[EUR][1000 genomes]
rs1194584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194585	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194586	0.90[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194587	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194592	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194607	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194608	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12029292	0.89[ASN][1000 genomes]
rs12033720	0.88[CEU][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12121085	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs1685606	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1685634	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1685635	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1760795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17654071	0.86[CHD][hapmap];0.84[GIH][hapmap]
rs1889312	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs2483712	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2633433	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28409746	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34870927	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4103781	0.87[EUR][1000 genomes]
rs72696290	0.88[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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription 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	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS 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	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1760794	THEM4	cis	parietal	SCAN
rs1760794	LCE1C	cis	cerebellum	SCAN
rs1760794	S100A4	cis	parietal	SCAN
rs1760794	VHLL	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154301400-154318400	Weak transcription	Small Intestine	intestine
2	chr1:154302200-154312200	Weak transcription	Gastric	stomach
3	chr1:154302200-154312600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:154302200-154322400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:154302400-154322400	Strong transcription	Dnd41	blood
6	chr1:154302400-154323200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:154302600-154314400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:154302600-154318200	Weak transcription	Fetal Heart	heart
9	chr1:154302600-154320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:154302600-154322600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:154302600-154323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:154302800-154323000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:154303000-154313000	Weak transcription	Colonic Mucosa	Colon
14	chr1:154303000-154322200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:154303000-154322600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:154303200-154312800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:154303200-154322200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:154303200-154322400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:154303200-154323400	Strong transcription	Fetal Brain Female	brain
20	chr1:154303200-154324600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:154304000-154322000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:154304200-154312600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:154304400-154312800	Weak transcription	Esophagus	oesophagus
24	chr1:154304800-154312600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:154304800-154317800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:154305800-154322200	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr1:154306200-154314200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:154306400-154322400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:154306800-154312000	Weak transcription	HSMM	muscle
30	chr1:154307200-154314600	Weak transcription	NHEK	skin
31	chr1:154307600-154311800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:154307600-154312400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:154307600-154314800	Strong transcription	HSMMtube	muscle
34	chr1:154307600-154322600	Strong transcription	Osteobl	bone
35	chr1:154307600-154324600	Weak transcription	Right Atrium	heart
36	chr1:154307800-154311800	Weak transcription	Spleen	Spleen
37	chr1:154307800-154312600	Weak transcription	Pancreas	Pancrea
38	chr1:154307800-154312800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:154307800-154316400	Weak transcription	Liver	Liver
40	chr1:154307800-154323200	Strong transcription	Fetal Stomach	stomach
41	chr1:154307800-154323200	Strong transcription	NHLF	lung
42	chr1:154308000-154312600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:154308000-154314600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr1:154308000-154321000	Weak transcription	Stomach Mucosa	stomach
45	chr1:154308000-154322600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:154308000-154323000	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:154308200-154314600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:154308200-154320600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:154308200-154322200	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:154308200-154323000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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