Variant report

Variant	rs4729598
Chromosome Location	chr7:100221867-100221868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100206101..100213131-chr7:100214394..100226559,23	K562	blood:
2	chr7:100200117..100203442-chr7:100221626..100226597,4	MCF-7	breast:
3	chr7:100181407..100183419-chr7:100221054..100223989,2	MCF-7	breast:
4	chr7:100217471..100219602-chr7:100221708..100224435,2	MCF-7	breast:
5	chr7:100221068..100223919-chr7:100274439..100277150,2	MCF-7	breast:
6	chr7:100209281..100214029-chr7:100217234..100224358,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172354	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000224729	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10247962	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1052897	1.00[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12673102	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1734907	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs221770	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs221774	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs221780	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs221784	0.85[CHB][hapmap]
rs221786	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs221789	1.00[JPT][hapmap]
rs221797	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs221803	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs3757859	1.00[ASW][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4727457	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4729600	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4988606	0.85[ASN][1000 genomes]
rs506597	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs564449	1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs6975957	1.00[JPT][hapmap]
rs7457868	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
3	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' 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	310 gene(s)	inside rSNPs	diseases
4	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
5	nsv888782	chr7:100064719-100236593	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
6	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
8	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv888790	chr7:100200674-100232387	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
10	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4729598	MYH16	cis	parietal	SCAN
rs4729598	TFR2	cis	lymphoblastoid	seeQTL
rs4729598	GNB2	cis	parietal	SCAN
rs4729598	TFR2	cis	multi-tissue	Pritchard
rs4729598	FBXO24	cis	cerebellum	SCAN
rs4729598	PDAP1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100210600-100224400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:100211000-100223800	Weak transcription	Fetal Kidney	kidney
3	chr7:100211000-100224600	Weak transcription	Small Intestine	intestine
4	chr7:100211200-100223800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:100211200-100224000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:100211200-100224000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:100211200-100224000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:100211200-100224000	Weak transcription	Brain Angular Gyrus	brain
9	chr7:100211200-100224000	Weak transcription	Lung	lung
10	chr7:100211200-100224000	Weak transcription	Psoas Muscle	Psoas
11	chr7:100211200-100224000	Weak transcription	Right Ventricle	heart
12	chr7:100211200-100224400	Weak transcription	Left Ventricle	heart
13	chr7:100211400-100223400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:100211400-100223800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:100211400-100224000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:100211400-100224000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:100211400-100224000	Weak transcription	Brain Substantia Nigra	brain
18	chr7:100211400-100224000	Weak transcription	Colonic Mucosa	Colon
19	chr7:100211400-100224000	Weak transcription	HSMM	muscle
20	chr7:100211400-100224000	Weak transcription	HUVEC	blood vessel
21	chr7:100211400-100224600	Weak transcription	Spleen	Spleen
22	chr7:100211400-100230400	Weak transcription	Pancreas	Pancrea
23	chr7:100211800-100223800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:100211800-100223800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:100211800-100224000	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:100212000-100223600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:100212000-100223600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr7:100212000-100223600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:100212000-100223800	Weak transcription	Fetal Brain Male	brain
30	chr7:100212200-100223800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:100212200-100223800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:100212200-100223800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:100212200-100224000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr7:100212600-100223400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr7:100212600-100224400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:100212800-100224000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:100212800-100224000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:100213200-100223600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:100213400-100223800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:100213600-100223800	Weak transcription	Fetal Lung	lung
41	chr7:100214600-100224000	Weak transcription	Gastric	stomach
42	chr7:100218600-100223400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:100218800-100224000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr7:100219600-100223800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr7:100219800-100223800	Weak transcription	Brain Anterior Caudate	brain
46	chr7:100220000-100223000	Weak transcription	HepG2	liver
47	chr7:100220000-100224000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr7:100220000-100224000	Weak transcription	Brain Germinal Matrix	brain
49	chr7:100220200-100223600	Weak transcription	Primary T cells from cord blood	blood
50	chr7:100220200-100223600	Weak transcription	Stomach Smooth Muscle	stomach

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