Variant report

Variant	rs1194585
Chromosome Location	chr1:154318564-154318565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:154318460-154318610	GM12874	blood:	n/a	n/a
2	CTCF	chr1:154318420-154318570	GM12870	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154299993..154302409-chr1:154316868..154319767,3	K562	blood:
2	chr1:154297478..154299656-chr1:154316954..154319172,2	MCF-7	breast:
3	chr1:154152480..154156086-chr1:154315865..154318822,4	MCF-7	breast:
4	chr1:154295903..154298479-chr1:154316522..154318683,2	K562	blood:

Variant related genes	Relation type
ATP8B2	TF binding region
ENSG00000143515	Chromatin interaction
ENSG00000143549	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	0.82[AMR][1000 genomes];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];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194586	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194587	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];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[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];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194607	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194608	1.00[AFR][1000 genomes];0.89[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];0.88[AFR][1000 genomes];0.83[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	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1685634	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1685635	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1760794	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]
rs1760795	0.83[AFR][1000 genomes];0.93[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];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2633433	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28409746	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34870927	0.92[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
rs1194585	VHLL	cis	cerebellum	SCAN
rs1194585	LCE1C	cis	cerebellum	SCAN
rs1194585	THEM4	cis	parietal	SCAN
rs1194585	S100A4	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154302200-154322400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:154302400-154322400	Strong transcription	Dnd41	blood
3	chr1:154302400-154323200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:154302600-154320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:154302600-154322600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:154302600-154323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:154302800-154323000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:154303000-154322200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:154303000-154322600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:154303200-154322200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:154303200-154322400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:154303200-154323400	Strong transcription	Fetal Brain Female	brain
13	chr1:154303200-154324600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:154304000-154322000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:154305800-154322200	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr1:154306400-154322400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:154307600-154322600	Strong transcription	Osteobl	bone
18	chr1:154307600-154324600	Weak transcription	Right Atrium	heart
19	chr1:154307800-154323200	Strong transcription	Fetal Stomach	stomach
20	chr1:154307800-154323200	Strong transcription	NHLF	lung
21	chr1:154308000-154321000	Weak transcription	Stomach Mucosa	stomach
22	chr1:154308000-154322600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:154308000-154323000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:154308200-154320600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:154308200-154322200	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:154308200-154323000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:154308200-154323200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:154308200-154323400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:154308600-154323000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:154309400-154322400	Strong transcription	Brain Cingulate Gyrus	brain
31	chr1:154309400-154322400	Strong transcription	NHDF-Ad	bronchial
32	chr1:154309600-154319200	Strong transcription	Aorta	Aorta
33	chr1:154309600-154319400	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr1:154309600-154319600	Strong transcription	NH-A	brain
35	chr1:154309600-154321800	Strong transcription	Fetal Lung	lung
36	chr1:154309600-154322200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:154309600-154322400	Strong transcription	Left Ventricle	heart
38	chr1:154309600-154322400	Strong transcription	Thymus	Thymus
39	chr1:154309600-154322800	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr1:154309600-154323000	Strong transcription	Brain Germinal Matrix	brain
41	chr1:154309600-154323200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr1:154309800-154319200	Strong transcription	Brain Hippocampus Middle	brain
43	chr1:154309800-154319200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:154309800-154319200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr1:154309800-154319600	Strong transcription	HepG2	liver
46	chr1:154309800-154321400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:154309800-154321400	Strong transcription	Placenta	Placenta
48	chr1:154309800-154322400	Strong transcription	Brain Angular Gyrus	brain
49	chr1:154309800-154322400	Strong transcription	Ovary	ovary
50	chr1:154309800-154322600	Strong transcription	Right Ventricle	heart

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