Variant report

Variant	rs2949096
Chromosome Location	chr7:66656379-66656380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10081276	0.80[EUR][1000 genomes]
rs10081331	0.80[EUR][1000 genomes]
rs10081333	0.80[EUR][1000 genomes]
rs10081344	0.80[EUR][1000 genomes]
rs10232876	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10233388	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10233507	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10247272	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10273692	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10277509	0.84[EUR][1000 genomes]
rs10950062	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10950064	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11761577	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11976638	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12155330	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2421393	0.82[AMR][1000 genomes]
rs2421398	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2421404	0.81[EUR][1000 genomes]
rs2421405	0.81[AMR][1000 genomes]
rs28808071	0.80[EUR][1000 genomes]
rs28860910	0.80[EUR][1000 genomes]
rs2901424	0.84[AMR][1000 genomes]
rs3107873	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34176733	0.80[EUR][1000 genomes]
rs34463275	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34566330	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs34567129	0.81[EUR][1000 genomes]
rs34574768	0.86[AMR][1000 genomes]
rs35064061	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35290283	0.89[AMR][1000 genomes]
rs35336066	0.83[EUR][1000 genomes]
rs35387955	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35521959	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs35918453	0.80[EUR][1000 genomes]
rs35970624	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3980790	0.84[AMR][1000 genomes]
rs4717354	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4718475	0.80[EUR][1000 genomes]
rs4718477	0.80[EUR][1000 genomes]
rs55921608	0.80[AMR][1000 genomes]
rs6947488	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6947514	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6948793	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6949429	0.80[EUR][1000 genomes]
rs6963793	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6967381	0.80[EUR][1000 genomes]
rs6967876	0.80[EUR][1000 genomes]
rs6979001	0.84[AMR][1000 genomes]
rs9886263	0.80[EUR][1000 genomes]
rs9986995	0.80[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	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv831019	chr7:66516808-66720485	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases
5	esv2422035	chr7:66621964-66676630	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1032237	chr7:66644492-66785029	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv970518	chr7:66647675-66742783	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2949096	GS1-124K5.4	cis	Nerve Tibial	GTEx
rs2949096	TYW1	Cis_1M	lymphoblastoid	RTeQTL
rs2949096	TYW1	cis	Nerve Tibial	GTEx
rs2949096	TYW1	cis	Heart Left Ventricle	GTEx
rs2949096	TYW1	cis	Muscle Skeletal	GTEx
rs2949096	TYW1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66621600-66672000	Weak transcription	Fetal Intestine Large	intestine
2	chr7:66628600-66684600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:66640600-66677200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:66643000-66660000	Weak transcription	Dnd41	blood
5	chr7:66644400-66659400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:66644400-66683000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:66644600-66659400	Weak transcription	Fetal Intestine Small	intestine
8	chr7:66644800-66660200	Weak transcription	Adipose Nuclei	Adipose
9	chr7:66645000-66657600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:66645000-66660000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:66645800-66660000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:66647000-66677400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr7:66647600-66657800	Weak transcription	Right Atrium	heart
14	chr7:66647600-66661400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr7:66647800-66659800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr7:66647800-66660000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:66648200-66679800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:66648800-66667200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:66649000-66658200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr7:66649200-66677200	Weak transcription	Right Ventricle	heart
21	chr7:66649200-66679200	Weak transcription	NHEK	skin
22	chr7:66650000-66660000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr7:66650200-66657800	Weak transcription	Ovary	ovary
24	chr7:66650600-66661800	Weak transcription	Fetal Stomach	stomach
25	chr7:66651200-66675400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:66651800-66657600	Weak transcription	GM12878-XiMat	blood
27	chr7:66652800-66675600	Weak transcription	Aorta	Aorta
28	chr7:66654000-66656400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr7:66654000-66656400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr7:66654000-66656600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr7:66654200-66656400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr7:66654200-66656400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr7:66654200-66656400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:66654200-66656400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr7:66654200-66656600	Enhancers	K562	blood
36	chr7:66654200-66658000	Enhancers	HSMMtube	muscle
37	chr7:66654200-66658200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr7:66654400-66657600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:66654400-66658200	Enhancers	Fetal Muscle Leg	muscle
40	chr7:66654400-66677400	Weak transcription	Esophagus	oesophagus
41	chr7:66654400-66681600	Weak transcription	Spleen	Spleen
42	chr7:66654600-66657600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:66654600-66658200	Weak transcription	Left Ventricle	heart
44	chr7:66654600-66660200	Weak transcription	Primary T cells from cord blood	blood
45	chr7:66654600-66660200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr7:66654600-66660200	Weak transcription	Fetal Kidney	kidney
47	chr7:66654600-66661400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:66654600-66678200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:66654600-66683400	Weak transcription	Pancreas	Pancrea
50	chr7:66654600-66684600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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