Variant report

Variant	rs3800815
Chromosome Location	chr7:66244981-66244982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10950047	0.81[ASN][1000 genomes]
rs10950055	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11766583	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs12666079	0.81[ASN][1000 genomes]
rs12668022	0.85[ASN][1000 genomes]
rs1638728	1.00[YRI][hapmap]
rs1638735	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17747939	0.87[ASN][1000 genomes]
rs17748121	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1796212	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1796218	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1796219	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1796226	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1796227	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1922722	0.83[ASN][1000 genomes]
rs2533284	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2707851	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2901267	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35244862	0.87[ASN][1000 genomes]
rs3735155	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4717322	0.98[ASN][1000 genomes]
rs4718385	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4718410	0.98[ASN][1000 genomes]
rs6960230	0.82[ASN][1000 genomes]
rs6966953	0.81[ASN][1000 genomes]
rs6970767	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6974046	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6979167	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73139927	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73139974	0.98[ASN][1000 genomes]
rs73377549	0.81[ASN][1000 genomes]
rs73377594	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv981512	chr7:66223352-66249901	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3800815	GS1-124K5.11	cis	Thyroid	GTEx
rs3800815	GS1-124K5.4	cis	Artery Aorta	GTEx
rs3800815	GTF2IRD1P1	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66207000-66255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:66231200-66246400	Weak transcription	Right Ventricle	heart
3	chr7:66231400-66255000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:66234800-66275800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:66235200-66261400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:66235400-66255400	Weak transcription	Fetal Heart	heart
8	chr7:66236000-66259000	Strong transcription	NHDF-Ad	bronchial
9	chr7:66236800-66245400	Strong transcription	GM12878-XiMat	blood
10	chr7:66236800-66247800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:66236800-66265200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr7:66236800-66276800	Strong transcription	Dnd41	blood
13	chr7:66236800-66277000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:66237000-66245000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr7:66237000-66245400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr7:66237200-66262400	Weak transcription	Fetal Brain Male	brain
18	chr7:66237200-66277600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:66238000-66246600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr7:66238000-66253800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr7:66238200-66246600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:66238200-66247600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:66238200-66248800	Strong transcription	Primary B cells from cord blood	blood
24	chr7:66238200-66252800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:66238200-66252800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr7:66238200-66276600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr7:66238400-66245000	Strong transcription	Fetal Muscle Leg	muscle
28	chr7:66238400-66247000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr7:66238400-66247800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr7:66238400-66248200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr7:66238400-66252800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr7:66238400-66252800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:66238600-66249200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr7:66238600-66255200	Weak transcription	Stomach Mucosa	stomach
35	chr7:66238800-66246400	Strong transcription	Adipose Nuclei	Adipose
36	chr7:66239200-66246400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr7:66239400-66245200	Strong transcription	Brain Hippocampus Middle	brain
38	chr7:66239800-66246400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:66239800-66254800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:66240000-66246600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr7:66240400-66260000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr7:66241000-66254800	Weak transcription	A549	lung
43	chr7:66241400-66250200	Weak transcription	Brain Angular Gyrus	brain
44	chr7:66241600-66247000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr7:66241600-66247400	Weak transcription	Gastric	stomach
46	chr7:66241800-66249000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:66242000-66246400	Weak transcription	Lung	lung
48	chr7:66242000-66246400	Weak transcription	Pancreas	Pancrea
49	chr7:66242000-66246400	Weak transcription	Thymus	Thymus
50	chr7:66242000-66252000	Weak transcription	Ovary	ovary

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