Variant report

Variant	rs6584149
Chromosome Location	chr10:99478081-99478082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99477505..99481349-chr10:99484055..99486700,3	MCF-7	breast:
2	chr10:99443080..99453237-chr10:99471420..99478243,12	MCF-7	breast:
3	chr10:99444102..99447131-chr10:99475724..99478855,3	MCF-7	breast:
4	chr10:99477514..99480441-chr10:99495281..99497954,2	MCF-7	breast:
5	chr10:99476839..99480454-chr10:99481730..99484335,3	K562	blood:
6	chr10:99476464..99480454-chr10:99480682..99484335,5	K562	blood:

Variant related genes	Relation type
ENSG00000155256	Chromatin interaction
ENSG00000119986	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10748706	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189342	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12415272	0.95[CHB][hapmap];0.92[CHD][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4593946	0.82[GIH][hapmap];0.84[MKK][hapmap]
rs4919133	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4919135	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6584148	0.90[CHB][hapmap];0.89[CHD][hapmap];0.82[AMR][1000 genomes]
rs7896853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7900119	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914697	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915100	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946780	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv519864	chr10:99478081-99486644	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6584149	FBXW4	cis	parietal	SCAN
rs6584149	MARVELD1	cis	lung	GTEx
rs6584149	MARVELD1	cis	Skin Sun Exposed Lower leg	GTEx
rs6584149	DHDPSL	cis	cerebellum	SCAN
rs6584149	ZFYVE27	cis	cerebellum	SCAN
rs6584149	MARVELD1	cis	Thyroid	GTEx
rs6584149	SEMA4G	cis	parietal	SCAN
rs6584149	C10orf62	cis	cerebellum	SCAN
rs6584149	PI4K2A	cis	parietal	SCAN
rs6584149	TLL2	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99473800-99479000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr10:99475000-99479400	Weak transcription	Fetal Kidney	kidney
3	chr10:99475200-99478200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:99475200-99478200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:99475200-99478200	Weak transcription	Pancreas	Pancrea
6	chr10:99475800-99478800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr10:99475800-99479200	Genic enhancers	Colon Smooth Muscle	Colon
8	chr10:99476000-99478400	Weak transcription	HSMMtube	muscle
9	chr10:99476000-99478800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr10:99476000-99479600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:99476000-99479600	Genic enhancers	Fetal Muscle Leg	muscle
12	chr10:99476000-99479600	Genic enhancers	Fetal Stomach	stomach
13	chr10:99476200-99479200	Genic enhancers	NHLF	lung
14	chr10:99476200-99479600	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr10:99476200-99486600	Weak transcription	Ovary	ovary
16	chr10:99476400-99478200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:99476400-99478400	Strong transcription	Fetal Lung	lung
18	chr10:99476400-99478600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr10:99476400-99478600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr10:99476400-99479600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:99476600-99478200	Genic enhancers	HMEC	breast
22	chr10:99476600-99478200	Genic enhancers	NHEK	skin
23	chr10:99476600-99478400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr10:99476600-99478600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr10:99476600-99479000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:99476600-99479000	Genic enhancers	NHDF-Ad	bronchial
27	chr10:99476600-99479200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr10:99476600-99479600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:99476600-99479800	Strong transcription	Osteobl	bone
30	chr10:99476600-99486200	Weak transcription	HUVEC	blood vessel
31	chr10:99476800-99478400	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr10:99477000-99478200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr10:99477000-99478200	Genic enhancers	Placenta	Placenta
34	chr10:99477000-99478400	Strong transcription	Dnd41	blood
35	chr10:99477000-99479000	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr10:99477000-99479000	Enhancers	Left Ventricle	heart
37	chr10:99477000-99479200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr10:99477000-99479600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr10:99477000-99480400	Enhancers	Colonic Mucosa	Colon
40	chr10:99477200-99478200	Enhancers	Brain Angular Gyrus	brain
41	chr10:99477200-99478600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr10:99477200-99479200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr10:99477200-99479600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr10:99477200-99479600	Enhancers	Stomach Mucosa	stomach
45	chr10:99477200-99479600	Enhancers	K562	blood
46	chr10:99477200-99486200	Weak transcription	NH-A	brain
47	chr10:99477400-99478200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr10:99477400-99478200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr10:99477400-99478200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr10:99477400-99478200	Enhancers	Brain Inferior Temporal Lobe	brain

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