Variant report

Variant	rs1695820
Chromosome Location	chr7:65844563-65844564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1000464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs1002053	0.88[CEU][hapmap]
rs10107	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs10215948	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs10224872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs10228885	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs10240949	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10250544	0.94[YRI][hapmap]
rs10255397	0.82[EUR][1000 genomes]
rs10256544	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs10257427	0.92[CEU][hapmap]
rs10260426	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs10261398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs10267430	0.92[CEU][hapmap]
rs10276077	0.84[EUR][1000 genomes]
rs10282433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs10447522	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10807704	0.82[EUR][1000 genomes]
rs1083554	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10950033	0.84[EUR][1000 genomes]
rs11760844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs11764589	0.83[EUR][1000 genomes]
rs11765965	0.87[CEU][hapmap]
rs11769079	0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11984115	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs12532998	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs12537823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs12673450	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs12698520	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs13536	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs1547529	0.82[YRI][hapmap]
rs1643375	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17138149	0.82[YRI][hapmap]
rs1875057	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs1909508	0.82[YRI][hapmap]
rs1968225	0.93[CEU][hapmap]
rs2036263	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2036264	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[YRI][hapmap]
rs2077593	0.93[CEU][hapmap]
rs2088653	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs2088655	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2173570	0.93[CEU][hapmap];0.90[YRI][hapmap]
rs2901152	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs2909688	0.82[EUR][1000 genomes]
rs3735148	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs4078376	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4149461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs4236208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[EUR][1000 genomes]
rs4587224	0.84[EUR][1000 genomes]
rs4718328	0.81[EUR][1000 genomes]
rs4718330	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs6460282	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs6460290	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6460292	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs6460293	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs6460296	0.93[CEU][hapmap]
rs6460302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6460304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6944374	0.96[CEU][hapmap];0.94[YRI][hapmap]
rs6945019	0.93[CEU][hapmap];0.80[CHB][hapmap]
rs6945032	0.92[CEU][hapmap]
rs6945843	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs6947339	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6950137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6951503	0.96[CEU][hapmap]
rs6952182	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs6955837	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs6956179	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs6959268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6960446	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs6962717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs6963228	0.83[EUR][1000 genomes]
rs6963646	0.92[CEU][hapmap]
rs6964437	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs6971509	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs6971752	0.84[EUR][1000 genomes]
rs6974614	1.00[CEU][hapmap]
rs6976714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[EUR][1000 genomes]
rs6978028	0.84[EUR][1000 genomes]
rs709595	0.93[CEU][hapmap]
rs709596	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7778322	0.82[EUR][1000 genomes]
rs7782704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7783613	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[YRI][hapmap]
rs7783779	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs778680	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778684	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778686	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778690	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs778697	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs778702	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs778703	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs778705	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs778706	0.93[CEU][hapmap]
rs778707	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs778711	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs778715	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778716	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778719	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778722	0.92[CEU][hapmap]
rs778724	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778728	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs778736	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7789615	0.82[EUR][1000 genomes]
rs7789768	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs7794930	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[YRI][hapmap]
rs7798630	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs801195	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs801204	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs809025	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs880166	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs937495	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[YRI][hapmap]
rs949930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	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
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking 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	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv970513	chr7:65842694-65860742	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv981506	chr7:65842694-65876873	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs1695820	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs1695820	RP4-756H11.3	cis	Thyroid	GTEx
rs1695820	RNU6-96P	cis	Thyroid	GTEx
rs1695820	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs1695820	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs1695820	RP4-756H11.3	cis	lung	GTEx
rs1695820	GS1-124K5.2	cis	Whole Blood	GTEx
rs1695820	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs1695820	GTF2IRD1P1	cis	Thyroid	GTEx
rs1695820	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs1695820	GS1-124K5.4	cis	Stomach	GTEx
rs1695820	GS1-124K5.11	cis	Thyroid	GTEx
rs1695820	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs1695820	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs1695820	RP4-756H11.3	cis	Artery Aorta	GTEx
rs1695820	RP4-756H11.3	cis	Artery Tibial	GTEx
rs1695820	LINC00174	cis	Thyroid	GTEx
rs1695820	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1695820	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65817600-65844600	Weak transcription	Fetal Brain Female	brain
2	chr7:65836600-65846400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:65838800-65844600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:65839000-65844800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:65839400-65844600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:65839800-65845200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr7:65840000-65878400	Weak transcription	Psoas Muscle	Psoas
8	chr7:65840200-65844800	Strong transcription	Fetal Muscle Leg	muscle
9	chr7:65840400-65873400	Weak transcription	K562	blood
10	chr7:65840600-65858400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:65841200-65847600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr7:65841400-65875400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:65841600-65845000	Strong transcription	Right Ventricle	heart
14	chr7:65841800-65844600	Weak transcription	Primary B cells from cord blood	blood
15	chr7:65841800-65844800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:65841800-65845400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:65842400-65845000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:65842400-65867800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr7:65842600-65844800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:65842600-65845400	Strong transcription	Fetal Intestine Large	intestine
21	chr7:65842600-65845400	Strong transcription	Pancreas	Pancrea
22	chr7:65842600-65845600	Strong transcription	Gastric	stomach
23	chr7:65842600-65846800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr7:65842800-65845000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:65842800-65845600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:65842800-65845600	Strong transcription	Brain Hippocampus Middle	brain
27	chr7:65842800-65845800	Strong transcription	Liver	Liver
28	chr7:65843000-65844800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:65843000-65844800	Strong transcription	Brain Germinal Matrix	brain
30	chr7:65843200-65844800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:65843200-65845400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr7:65843200-65847200	Weak transcription	Fetal Brain Male	brain
33	chr7:65843400-65845000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:65843400-65845200	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr7:65843400-65845200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:65843400-65877600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr7:65843600-65844800	Strong transcription	Colonic Mucosa	Colon
38	chr7:65843600-65845600	ZNF genes & repeats	Fetal Stomach	stomach
39	chr7:65843600-65878200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:65843800-65844600	Strong transcription	Adipose Nuclei	Adipose
41	chr7:65843800-65844800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr7:65843800-65845000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:65843800-65845000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr7:65843800-65845000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:65843800-65845200	ZNF genes & repeats	Aorta	Aorta
46	chr7:65843800-65845200	ZNF genes & repeats	Lung	lung
47	chr7:65843800-65845400	Strong transcription	Primary T cells from cord blood	blood
48	chr7:65843800-65845400	Strong transcription	Brain Angular Gyrus	brain
49	chr7:65843800-65845600	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr7:65843800-65845600	Strong transcription	Brain Substantia Nigra	brain

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