Variant report

Variant	rs1194587
Chromosome Location	chr1:154317153-154317154
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154300114..154302285-chr1:154316277..154318488,2	MCF-7	breast:
2	chr1:154317108..154317820-chr1:154438724..154439547,2	MCF-7	breast:
3	chr1:154308881..154311525-chr1:154315702..154317705,2	K562	blood:
4	chr1:154299993..154302409-chr1:154316868..154319767,3	K562	blood:
5	chr1:154297478..154299656-chr1:154316954..154319172,2	MCF-7	breast:
6	chr1:154152480..154156086-chr1:154315865..154318822,4	MCF-7	breast:
7	chr1:154315444..154317958-chr1:154431892..154433961,2	MCF-7	breast:
8	chr1:154314633..154318404-chr1:154324088..154325783,3	K562	blood:
9	chr1:154295903..154298479-chr1:154316522..154318683,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238365	Chromatin interaction
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	0.84[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];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194585	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]
rs1194586	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][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];0.95[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];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194608	1.00[AFR][1000 genomes];0.91[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];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12121085	0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs1685606	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1685634	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1685635	0.88[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];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]
rs1760795	0.83[AFR][1000 genomes];0.96[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];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2633433	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28409746	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34870927	0.95[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
rs1194587	LCE1C	cis	cerebellum	SCAN
rs1194587	THEM4	cis	parietal	SCAN
rs1194587	VHLL	cis	cerebellum	SCAN
rs1194587	S100A4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154301400-154318400	Weak transcription	Small Intestine	intestine
2	chr1:154302200-154322400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154302400-154322400	Strong transcription	Dnd41	blood
4	chr1:154302400-154323200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:154302600-154318200	Weak transcription	Fetal Heart	heart
6	chr1:154302600-154320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:154302600-154322600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:154302600-154323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:154302800-154323000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:154303000-154322200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:154303000-154322600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:154303200-154322200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:154303200-154322400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:154303200-154323400	Strong transcription	Fetal Brain Female	brain
15	chr1:154303200-154324600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:154304000-154322000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:154304800-154317800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:154305800-154322200	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr1:154306400-154322400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:154307600-154322600	Strong transcription	Osteobl	bone
21	chr1:154307600-154324600	Weak transcription	Right Atrium	heart
22	chr1:154307800-154323200	Strong transcription	Fetal Stomach	stomach
23	chr1:154307800-154323200	Strong transcription	NHLF	lung
24	chr1:154308000-154321000	Weak transcription	Stomach Mucosa	stomach
25	chr1:154308000-154322600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:154308000-154323000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:154308200-154320600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:154308200-154322200	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:154308200-154323000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:154308200-154323200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:154308200-154323400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:154308600-154323000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:154309400-154322400	Strong transcription	Brain Cingulate Gyrus	brain
34	chr1:154309400-154322400	Strong transcription	NHDF-Ad	bronchial
35	chr1:154309600-154319200	Strong transcription	Aorta	Aorta
36	chr1:154309600-154319400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr1:154309600-154319600	Strong transcription	NH-A	brain
38	chr1:154309600-154321800	Strong transcription	Fetal Lung	lung
39	chr1:154309600-154322200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:154309600-154322400	Strong transcription	Left Ventricle	heart
41	chr1:154309600-154322400	Strong transcription	Thymus	Thymus
42	chr1:154309600-154322800	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr1:154309600-154323000	Strong transcription	Brain Germinal Matrix	brain
44	chr1:154309600-154323200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr1:154309800-154319200	Strong transcription	Brain Hippocampus Middle	brain
46	chr1:154309800-154319200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:154309800-154319200	Strong transcription	Rectal Smooth Muscle	rectum
48	chr1:154309800-154319600	Strong transcription	HepG2	liver
49	chr1:154309800-154321400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:154309800-154321400	Strong transcription	Placenta	Placenta

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