Variant report

Variant	rs6702754
Chromosome Location	chr1:154303976-154303977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154154470..154156180-chr1:154303921..154306139,2	MCF-7	breast:
2	chr1:154301040..154304335-chr1:154309259..154312100,3	K562	blood:
3	chr1:154297523..154301046-chr1:154302603..154305255,3	K562	blood:

Variant related genes	Relation type
ENSG00000238365	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143515	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12077870	1.00[CHB][hapmap];1.00[JPT][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]
rs12727865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12748146	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35950207	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3890153	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6672010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6685323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6688376	0.81[ASW][hapmap];0.93[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv523934	chr1:154296076-154307630	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6702754	DENND4B	cis	cerebellum	SCAN
rs6702754	CREB3L4	cis	parietal	SCAN
rs6702754	SLC27A3	cis	parietal	SCAN
rs6702754	NPR1	cis	parietal	SCAN
rs6702754	S100A6	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154301000-154308400	Weak transcription	Fetal Kidney	kidney
2	chr1:154301200-154304000	Weak transcription	NHEK	skin
3	chr1:154301400-154318400	Weak transcription	Small Intestine	intestine
4	chr1:154301800-154304000	Weak transcription	Ovary	ovary
5	chr1:154301800-154304000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:154301800-154306800	Weak transcription	Right Atrium	heart
7	chr1:154301800-154307400	Weak transcription	Pancreas	Pancrea
8	chr1:154302000-154304000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:154302000-154306800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:154302200-154312200	Weak transcription	Gastric	stomach
11	chr1:154302200-154312600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:154302200-154322400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:154302400-154304000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:154302400-154304800	Strong transcription	Fetal Lung	lung
15	chr1:154302400-154305400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:154302400-154305400	Strong transcription	Colon Smooth Muscle	Colon
17	chr1:154302400-154305600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:154302400-154306000	Strong transcription	NHLF	lung
19	chr1:154302400-154306400	Weak transcription	Liver	Liver
20	chr1:154302400-154306400	Strong transcription	NHDF-Ad	bronchial
21	chr1:154302400-154322400	Strong transcription	Dnd41	blood
22	chr1:154302400-154323200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:154302600-154304200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:154302600-154304600	Strong transcription	K562	blood
25	chr1:154302600-154305000	Strong transcription	HepG2	liver
26	chr1:154302600-154306200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:154302600-154306200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:154302600-154306400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:154302600-154306400	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:154302600-154306600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:154302600-154307000	Strong transcription	Fetal Stomach	stomach
32	chr1:154302600-154309800	Weak transcription	Fetal Brain Male	brain
33	chr1:154302600-154314400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:154302600-154318200	Weak transcription	Fetal Heart	heart
35	chr1:154302600-154320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:154302600-154322600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:154302600-154323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:154302800-154304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:154302800-154305400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:154302800-154305800	Strong transcription	Placenta	Placenta
41	chr1:154302800-154306600	Strong transcription	Osteobl	bone
42	chr1:154302800-154307600	Strong transcription	Aorta	Aorta
43	chr1:154302800-154307800	Strong transcription	Brain Germinal Matrix	brain
44	chr1:154302800-154323000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:154303000-154304600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:154303000-154304800	Strong transcription	Right Ventricle	heart
47	chr1:154303000-154305400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:154303000-154305400	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr1:154303000-154305400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr1:154303000-154305400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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