Variant report

Variant	rs3849654
Chromosome Location	chr4:53986081-53986082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53978972..53981461-chr4:53984171..53987382,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10028181	0.83[JPT][hapmap]
rs1038355	0.82[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.83[EUR][1000 genomes]
rs10517275	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs11133243	0.83[JPT][hapmap]
rs11732744	0.85[EUR][1000 genomes]
rs11931066	0.84[EUR][1000 genomes]
rs11934112	0.81[CEU][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.85[EUR][1000 genomes]
rs11947923	0.82[GIH][hapmap]
rs12506298	0.85[EUR][1000 genomes]
rs17082398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2046306	0.84[EUR][1000 genomes]
rs2046307	0.82[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes]
rs28770187	0.87[EUR][1000 genomes]
rs4241973	0.83[JPT][hapmap]
rs4302515	0.81[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4314341	0.84[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4320191	1.00[ASW][hapmap];0.81[CEU][hapmap];0.88[GIH][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4479763	0.85[EUR][1000 genomes]
rs4864723	0.80[YRI][hapmap]
rs59629308	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66506011	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6811236	0.85[EUR][1000 genomes]
rs6822251	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6843335	0.82[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.84[EUR][1000 genomes]
rs6846933	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs6847431	0.82[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs72624189	0.86[EUR][1000 genomes]
rs72624190	0.88[EUR][1000 genomes]
rs72624191	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7378381	0.82[JPT][hapmap]
rs7662427	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs7676982	0.82[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap]
rs998264	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3849654	HOPX	cis	parietal	SCAN
rs3849654	KIT	cis	parietal	SCAN
rs3849654	CLIC6	trans	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53978800-54008000	Weak transcription	Primary T cells from cord blood	blood
2	chr4:53980000-53986800	Weak transcription	Aorta	Aorta
3	chr4:53980400-53993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:53982200-53989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:53983200-53987400	Weak transcription	Ovary	ovary
6	chr4:53984600-53986600	Enhancers	Fetal Heart	heart
7	chr4:53984600-53986800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:53984800-53986400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr4:53984800-53989600	Enhancers	Brain Substantia Nigra	brain
10	chr4:53985200-53986200	Weak transcription	Colonic Mucosa	Colon
11	chr4:53985200-53986200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:53985200-53988200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:53985400-53986200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:53985400-53986800	Enhancers	Placenta	Placenta
15	chr4:53985600-53986400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:53985600-53986400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:53985600-53986600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr4:53985600-53986600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:53985600-53986600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:53985600-53986600	Enhancers	HSMM	muscle
21	chr4:53985600-53986600	Enhancers	NH-A	brain
22	chr4:53985600-53986800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:53985600-53986800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:53985600-53986800	Enhancers	Fetal Intestine Large	intestine
25	chr4:53985600-53987000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:53985600-53987000	Enhancers	NHDF-Ad	bronchial
27	chr4:53985600-53987200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:53985600-53988000	Enhancers	Osteobl	bone
29	chr4:53985600-53989600	Enhancers	Fetal Intestine Small	intestine
30	chr4:53985600-53990200	Enhancers	Stomach Mucosa	stomach
31	chr4:53985600-53991400	Enhancers	HepG2	liver
32	chr4:53985800-53986200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:53985800-53986200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr4:53985800-53986200	Enhancers	Brain Cingulate Gyrus	brain
35	chr4:53985800-53986200	Enhancers	Fetal Kidney	kidney
36	chr4:53985800-53986400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:53985800-53986400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr4:53985800-53986400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr4:53985800-53986400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:53985800-53986400	Enhancers	Brain Hippocampus Middle	brain
41	chr4:53985800-53986400	Enhancers	Fetal Muscle Leg	muscle
42	chr4:53985800-53986400	Enhancers	Hela-S3	cervix
43	chr4:53985800-53986400	Enhancers	HMEC	breast
44	chr4:53985800-53986600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:53985800-53986600	Enhancers	NHEK	skin
46	chr4:53985800-53986800	Enhancers	Placenta Amnion	Placenta Amnion
47	chr4:53985800-53986800	Enhancers	HSMMtube	muscle
48	chr4:53985800-53987600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr4:53985800-53987800	Enhancers	NHLF	lung
50	chr4:53985800-53988600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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