Variant report

Variant	rs7550843
Chromosome Location	chr1:113452233-113452234
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113448862..113452902-chr1:113455376..113458880,4	K562	blood:
2	chr1:113450799..113452592-chr1:113464011..113465948,2	K562	blood:
3	chr1:113452222..113455252-chr1:113457293..113459554,4	K562	blood:

Variant related genes	Relation type
ENSG00000155380	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11102560	0.92[EUR][1000 genomes]
rs12064292	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12126192	0.92[EUR][1000 genomes]
rs1216537	0.81[CEU][hapmap]
rs17440299	1.00[CEU][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs17493313	1.00[CEU][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs17494145	0.91[CEU][hapmap]
rs17494180	0.91[CEU][hapmap]
rs1936311	0.95[EUR][1000 genomes]
rs2149036	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs28556822	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs3849174	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4838971	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4839270	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4839272	1.00[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs4839276	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs55768060	0.82[EUR][1000 genomes]
rs55982206	0.84[EUR][1000 genomes]
rs55992320	0.95[EUR][1000 genomes]
rs56007797	0.95[EUR][1000 genomes]
rs56019044	0.85[EUR][1000 genomes]
rs56220197	0.91[EUR][1000 genomes]
rs6676446	0.88[EUR][1000 genomes]
rs6676864	0.91[EUR][1000 genomes]
rs66899043	0.94[EUR][1000 genomes]
rs72683432	0.94[EUR][1000 genomes]
rs72683434	0.95[EUR][1000 genomes]
rs72683442	0.96[EUR][1000 genomes]
rs72683453	0.91[EUR][1000 genomes]
rs72683454	0.93[EUR][1000 genomes]
rs72683459	0.85[EUR][1000 genomes]
rs7518984	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7524567	0.94[EUR][1000 genomes]
rs7536532	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7540321	0.89[EUR][1000 genomes]
rs7542229	0.97[EUR][1000 genomes]
rs7545602	0.95[EUR][1000 genomes]
rs7548109	0.89[EUR][1000 genomes]
rs7552903	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9429505	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9429709	0.83[ASW][hapmap];1.00[CEU][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.95[EUR][1000 genomes]
rs9429710	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7550843	OVGP1	cis	cerebellum	SCAN
rs7550843	DDX20	cis	cerebellum	SCAN
rs7550843	SLC16A1	Cis_1M	lymphoblastoid	RTeQTL
rs7550843	LRIG2	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113439200-113459200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:113439200-113460400	Weak transcription	Aorta	Aorta
3	chr1:113440200-113456400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:113440400-113459600	Weak transcription	Primary T cells from cord blood	blood
5	chr1:113444400-113454400	Weak transcription	HepG2	liver
6	chr1:113444400-113456600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:113446000-113456600	Weak transcription	Fetal Heart	heart
8	chr1:113446200-113455600	Weak transcription	A549	lung
9	chr1:113446400-113457800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:113446600-113459600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:113446800-113459800	Weak transcription	Psoas Muscle	Psoas
12	chr1:113447000-113452800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:113447000-113454600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:113447200-113455400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:113447200-113456000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:113447200-113456400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:113447400-113452600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:113447400-113459200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:113447400-113459600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:113447600-113456200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:113447800-113452400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:113447800-113457800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:113447800-113458000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:113447800-113459600	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:113447800-113470200	Weak transcription	Fetal Kidney	kidney
26	chr1:113448200-113457800	Weak transcription	Ovary	ovary
27	chr1:113448400-113457800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:113448600-113452800	Weak transcription	Dnd41	blood
29	chr1:113448600-113457600	Weak transcription	NHDF-Ad	bronchial
30	chr1:113448800-113452600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:113448800-113454400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:113448800-113455600	Weak transcription	GM12878-XiMat	blood
33	chr1:113448800-113458600	Weak transcription	Fetal Stomach	stomach
34	chr1:113448800-113459400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:113449000-113452600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:113449000-113452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:113449000-113452800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:113449000-113453000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:113449000-113454200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:113449000-113455200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:113449000-113455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:113449000-113456200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:113449000-113456400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr1:113449000-113456400	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:113449000-113456400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:113449000-113456600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:113449000-113457800	Weak transcription	Left Ventricle	heart
48	chr1:113449000-113457800	Weak transcription	Right Ventricle	heart
49	chr1:113449000-113457800	Weak transcription	NHLF	lung
50	chr1:113449000-113458000	Weak transcription	Primary B cells from cord blood	blood

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