Variant report

Variant	rs7800335
Chromosome Location	chr7:128253396-128253397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1013514	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs101721	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs10488628	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs10954206	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11769769	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11982488	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2956682	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4731481	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55817807	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55928948	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59287454	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60382581	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61437980	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62481896	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62481928	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62483311	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62483370	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6467200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6467202	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6467203	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6955870	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6965333	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6978360	0.80[ASN][1000 genomes]
rs6979304	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6979575	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7795141	0.84[ASN][1000 genomes]
rs9768325	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv966885	chr7:128212815-128256300	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs7800335	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs7800335	CICP14	cis	Skin Sun Exposed Lower leg	GTEx
rs7800335	RP11-274B21.3	cis	Muscle Skeletal	GTEx
rs7800335	RP11-274B21.1	cis	Nerve Tibial	GTEx
rs7800335	RP11-274B21.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7800335	RP11-274B21.4	cis	Nerve Tibial	GTEx
rs7800335	RP11-274B21.4	cis	Muscle Skeletal	GTEx
rs7800335	RP11-274B21.2	cis	lung	GTEx
rs7800335	RP11-274B21.3	cis	Thyroid	GTEx
rs7800335	TMEM209	cis	parietal	SCAN
rs7800335	RP11-274B21.4	cis	Esophagus Mucosa	GTEx
rs7800335	RP11-274B21.2	cis	Muscle Skeletal	GTEx
rs7800335	CICP14	cis	Thyroid	GTEx
rs7800335	RP11-274B21.4	cis	lung	GTEx
rs7800335	RP11-274B21.4	cis	Stomach	GTEx
rs7800335	RP11-274B21.1	cis	lung	GTEx
rs7800335	C7orf54	cis	cerebellum	SCAN
rs7800335	RP11-274B21.2	cis	Stomach	GTEx
rs7800335	RP11-274B21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs7800335	RP11-274B21.3	cis	Nerve Tibial	GTEx
rs7800335	TSGA14	cis	cerebellum	SCAN
rs7800335	CICP14	cis	Artery Tibial	GTEx
rs7800335	RP11-274B21.2	cis	Thyroid	GTEx
rs7800335	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs7800335	RP11-274B21.2	cis	Nerve Tibial	GTEx
rs7800335	RP11-274B21.4	cis	Skin Sun Exposed Lower leg	GTEx
rs7800335	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs7800335	RP11-274B21.4	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128200000-128258800	Weak transcription	Right Ventricle	heart
2	chr7:128204800-128258800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:128223800-128258800	Weak transcription	Lung	lung
4	chr7:128226400-128258800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:128233200-128258800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:128233200-128258800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:128233400-128258400	Weak transcription	Thymus	Thymus
8	chr7:128233400-128258600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:128233400-128258800	Weak transcription	Aorta	Aorta
10	chr7:128233400-128258800	Weak transcription	Esophagus	oesophagus
11	chr7:128233400-128258800	Weak transcription	Spleen	Spleen
12	chr7:128233400-128259000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:128233400-128259000	Weak transcription	Colon Smooth Muscle	Colon
14	chr7:128233400-128259600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:128233400-128272000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:128233600-128258800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:128233800-128257600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:128233800-128258800	Weak transcription	Fetal Brain Female	brain
19	chr7:128234600-128257600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:128234600-128258800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:128234600-128258800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:128234600-128258800	Weak transcription	Gastric	stomach
23	chr7:128234600-128271200	Weak transcription	Fetal Lung	lung
24	chr7:128235000-128253800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr7:128235600-128258800	Weak transcription	Pancreas	Pancrea
26	chr7:128237600-128256600	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:128237600-128258600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:128237800-128290400	Weak transcription	HepG2	liver
29	chr7:128238200-128258800	Weak transcription	Ovary	ovary
30	chr7:128239200-128256000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr7:128239200-128287200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr7:128239200-128296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr7:128239400-128258800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr7:128239400-128271200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:128239600-128258800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:128239600-128262400	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:128239800-128257600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:128239800-128258800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr7:128240000-128255600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr7:128240000-128258800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr7:128240200-128269400	Weak transcription	Primary B cells from cord blood	blood
42	chr7:128240400-128253400	Weak transcription	Brain Substantia Nigra	brain
43	chr7:128240400-128258800	Weak transcription	Primary T cells from cord blood	blood
44	chr7:128242600-128292800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr7:128246200-128254000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:128246600-128284800	Weak transcription	Stomach Mucosa	stomach
47	chr7:128247000-128254200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr7:128247000-128256000	Weak transcription	Fetal Intestine Large	intestine
49	chr7:128247000-128258800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:128247200-128255400	Weak transcription	Duodenum Mucosa	Duodenum

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