Variant report

Variant	rs60229418
Chromosome Location	chr7:128294449-128294450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:128294405-128294455	Caco-2	colon:	n/a
2	chr7:128294405-128294455	T-47D	breast:	n/a
3	chr7:128294405-128294455	HMEC	breast:	n/a
4	chr7:128294405-128294455	HepG2	liver:	n/a
5	chr7:128294405-128294455	H1-hESC	embryonic stem cell:	embryo
6	chr7:128294405-128294455	HEK293	kidney:	embryo
7	chr7:128294405-128294455	ovcar-3	ovarian:	n/a
8	chr7:128294405-128294455	HCT-116	colon:	n/a
9	chr7:128294405-128294455	A549	lung:	n/a
10	chr7:128294405-128294455	CMK	blood:	n/a
11	chr7:128294405-128294455	HCPEpiC	choroid plexus:	n/a
12	chr7:128294405-128294455	AG09309	skin:	n/a
13	chr7:128294405-128294455	HL-60	blood:	n/a
14	chr7:128294405-128294455	NT2-D1	testis:	n/a
15	chr7:128294405-128294455	AG09319	gingival:	n/a
16	chr7:128294405-128294455	NHDF-neo	bronchial:	n/a
17	chr7:128294405-128294455	MCF10A-Er-Src	breast:	n/a
18	chr7:128294405-128294455	ECC-1	luminal epithelium:	n/a
19	chr7:128294405-128294455	IMR90	lung:	fetal
20	chr7:128294405-128294455	AG04450	lung:	fetal
21	chr7:128294405-128294455	HPAEpiC	pulmonary alveolar:	n/a
22	chr7:128294405-128294455	GM06990	blood:	n/a
23	chr7:128294405-128294455	NH-A	brain:	n/a
24	chr7:128294405-128294455	K562	blood:	n/a
25	chr7:128294405-128294455	PFSK-1	brain:	n/a
26	chr7:128294405-128294455	PrEC	prostate:	n/a
27	chr7:128294405-128294455	GM12878	blood:	n/a
28	chr7:128294405-128294455	PANC-1	pancreas:	n/a
29	chr7:128294405-128294455	GM12891	blood:	n/a
30	chr7:128294405-128294455	SK-N-MC	brain:	n/a
31	chr7:128294405-128294455	HNPCEpiC	eye:	n/a
32	chr7:128294405-128294455	MCF-7	breast:	n/a
33	chr7:128294405-128294455	AG04449	skin:	fetal
34	chr7:128294405-128294455	NB4	blood:	n/a
35	chr7:128294405-128294455	BJ	skin:	n/a
36	chr7:128294405-128294455	HCM	heart:	n/a
37	chr7:128294405-128294455	LNCaP	prostate:	n/a
38	chr7:128294405-128294455	HRPEpiC	eye:	n/a
39	chr7:128294405-128294455	U87	brain:	n/a
40	chr7:128294405-128294455	AG10803	skin:	n/a
41	chr7:128294405-128294455	NHBE	bronchial:	n/a
42	chr7:128294405-128294455	ProgFib	skin:	n/a
43	chr7:128294405-128294455	Hela-S3	cervix:	n/a
44	chr7:128294405-128294455	HAEpiC	amniotic membrane:	n/a
45	chr7:128294405-128294455	SKMC	muscle:	n/a
46	chr7:128294405-128294455	GM19239	blood:	n/a
47	chr7:128294405-128294455	HRE	kidney:	n/a
48	chr7:128294405-128294455	HIPEpiC	eye:	n/a
49	chr7:128294405-128294455	GM12892	blood:	n/a
50	chr7:128294405-128294455	SAEC	small airway:	n/a

No data

Variant related genes	Relation type
ENSG00000229413	CpG island

Extended variants
information (count: 165 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs1003241	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10215560	0.87[EUR][1000 genomes]
rs10215566	0.87[EUR][1000 genomes]
rs10215947	0.87[EUR][1000 genomes]
rs10229874	0.85[EUR][1000 genomes]
rs10237278	0.85[EUR][1000 genomes]
rs10464537	0.81[EUR][1000 genomes]
rs10464538	0.81[EUR][1000 genomes]
rs10954193	0.85[EUR][1000 genomes]
rs10954194	0.88[EUR][1000 genomes]
rs10954195	0.88[EUR][1000 genomes]
rs1109552	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11971248	0.85[EUR][1000 genomes]
rs11975784	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11977129	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11979586	0.87[EUR][1000 genomes]
rs12667202	0.82[EUR][1000 genomes]
rs12670258	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12670271	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12670432	0.82[EUR][1000 genomes]
rs12671767	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12672443	0.82[EUR][1000 genomes]
rs12672518	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12672529	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12672576	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12672608	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12672940	0.80[EUR][1000 genomes]
rs12673048	0.82[EUR][1000 genomes]
rs12673060	0.82[EUR][1000 genomes]
rs12673998	0.87[EUR][1000 genomes]
rs12674125	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13438170	0.85[EUR][1000 genomes]
rs1450874	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17169024	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17169357	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17169368	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17169609	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17533628	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1809082	0.87[EUR][1000 genomes]
rs1839593	0.80[EUR][1000 genomes]
rs1970827	0.87[EUR][1000 genomes]
rs1970828	0.86[EUR][1000 genomes]
rs2044834	0.87[EUR][1000 genomes]
rs2290229	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2402907	0.87[EUR][1000 genomes]
rs2443110	0.81[EUR][1000 genomes]
rs3213979	0.84[EUR][1000 genomes]
rs34614236	0.85[EUR][1000 genomes]
rs35394926	0.87[EUR][1000 genomes]
rs3857849	0.87[EUR][1000 genomes]
rs3896308	0.86[EUR][1000 genomes]
rs3927852	0.87[EUR][1000 genomes]
rs3931943	0.87[EUR][1000 genomes]
rs4077398	0.83[EUR][1000 genomes]
rs4079001	0.87[EUR][1000 genomes]
rs4079003	0.86[EUR][1000 genomes]
rs4260830	0.83[EUR][1000 genomes]
rs4554406	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4562239	0.82[EUR][1000 genomes]
rs4579449	0.81[EUR][1000 genomes]
rs4728128	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4728130	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4731482	0.82[EUR][1000 genomes]
rs4731484	0.85[EUR][1000 genomes]
rs4731486	0.85[EUR][1000 genomes]
rs4731488	0.87[EUR][1000 genomes]
rs4731492	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4731493	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4731496	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4731497	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4731500	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4731501	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4731503	0.80[AMR][1000 genomes]
rs4731504	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4731506	0.80[AMR][1000 genomes]
rs55860694	0.82[EUR][1000 genomes]
rs55978216	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55982013	0.81[EUR][1000 genomes]
rs56030011	0.82[EUR][1000 genomes]
rs56052829	0.84[EUR][1000 genomes]
rs56111366	0.82[EUR][1000 genomes]
rs56189614	0.84[EUR][1000 genomes]
rs56278047	0.84[EUR][1000 genomes]
rs56329625	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56916616	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56946745	0.86[EUR][1000 genomes]
rs57226192	0.83[EUR][1000 genomes]
rs57370656	0.87[EUR][1000 genomes]
rs57653865	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57886720	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58123072	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58133562	0.82[EUR][1000 genomes]
rs59066415	0.82[EUR][1000 genomes]
rs59154282	0.84[EUR][1000 genomes]
rs59594227	0.82[EUR][1000 genomes]
rs60473286	0.81[EUR][1000 genomes]
rs60515997	0.82[EUR][1000 genomes]
rs60781570	0.80[EUR][1000 genomes]
rs61146845	0.82[EUR][1000 genomes]
rs61312980	0.82[EUR][1000 genomes]
rs61318942	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61738927	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62479751	0.84[EUR][1000 genomes]
rs62479756	0.84[EUR][1000 genomes]
rs62479757	0.84[EUR][1000 genomes]
rs62481868	0.87[EUR][1000 genomes]
rs62481869	0.87[EUR][1000 genomes]
rs62481873	0.87[EUR][1000 genomes]
rs62481883	0.87[EUR][1000 genomes]
rs62481890	0.87[EUR][1000 genomes]
rs62481892	0.87[EUR][1000 genomes]
rs62481895	0.87[EUR][1000 genomes]
rs62481897	0.86[EUR][1000 genomes]
rs62481901	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62481902	0.82[EUR][1000 genomes]
rs62481906	0.85[EUR][1000 genomes]
rs62481907	0.80[EUR][1000 genomes]
rs62481926	0.81[AMR][1000 genomes]
rs62481938	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62481939	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62481940	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62483293	0.80[EUR][1000 genomes]
rs62483298	0.80[EUR][1000 genomes]
rs62483302	0.82[EUR][1000 genomes]
rs62483305	0.82[EUR][1000 genomes]
rs62483364	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62483366	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6467185	0.82[EUR][1000 genomes]
rs6467186	0.82[EUR][1000 genomes]
rs6467188	0.85[EUR][1000 genomes]
rs6467189	0.85[EUR][1000 genomes]
rs6467194	0.85[EUR][1000 genomes]
rs6467195	0.87[EUR][1000 genomes]
rs6467196	0.83[EUR][1000 genomes]
rs6467204	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6467206	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6467209	0.83[EUR][1000 genomes]
rs6467210	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67602452	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6945532	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6954284	0.84[EUR][1000 genomes]
rs6954404	0.85[EUR][1000 genomes]
rs6958788	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6969462	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6969528	0.82[EUR][1000 genomes]
rs6969554	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6973969	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6978887	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73236020	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73236037	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7385007	0.84[EUR][1000 genomes]
rs7385683	0.81[EUR][1000 genomes]
rs7781695	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7786336	0.82[EUR][1000 genomes]
rs7792915	0.87[EUR][1000 genomes]
rs7793136	0.87[EUR][1000 genomes]
rs7797745	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9640850	0.82[EUR][1000 genomes]
rs9641824	0.82[EUR][1000 genomes]
rs9641826	0.81[EUR][1000 genomes]
rs9801409	0.81[AMR][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	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	nsv970938	chr7:128256300-128300276	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv981680	chr7:128288269-128298277	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv993870	chr7:128292907-128295065	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:33)

SNP	Gene	Cis/trans	Tissue	Source
rs60229418	RP11-274B21.4	cis	Stomach	GTEx
rs60229418	RP11-274B21.2	cis	Muscle Skeletal	GTEx
rs60229418	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs60229418	RP11-274B21.4	cis	Thyroid	GTEx
rs60229418	RP11-274B21.4	cis	Esophagus Muscularis	GTEx
rs60229418	RP11-274B21.10	cis	Whole Blood	GTEx
rs60229418	RP11-274B21.3	cis	Muscle Skeletal	GTEx
rs60229418	RP11-274B21.2	cis	lung	GTEx
rs60229418	RP11-274B21.1	cis	Thyroid	GTEx
rs60229418	RP11-274B21.1	cis	Muscle Skeletal	GTEx
rs60229418	RP11-274B21.1	cis	Nerve Tibial	GTEx
rs60229418	RP11-274B21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs60229418	RP11-274B21.9	cis	Esophagus Mucosa	GTEx
rs60229418	METTL2B	cis	Skin Sun Exposed Lower leg	GTEx
rs60229418	RP11-274B21.1	cis	lung	GTEx
rs60229418	RP11-274B21.1	cis	Whole Blood	GTEx
rs60229418	RP11-274B21.4	cis	Whole Blood	GTEx
rs60229418	RP11-274B21.4	cis	Skin Sun Exposed Lower leg	GTEx
rs60229418	RP11-274B21.1	cis	Artery Tibial	GTEx
rs60229418	RP11-274B21.2	cis	Esophagus Muscularis	GTEx
rs60229418	RP11-274B21.2	cis	Artery Tibial	GTEx
rs60229418	RP11-274B21.1	cis	Esophagus Muscularis	GTEx
rs60229418	RP11-274B21.4	cis	Muscle Skeletal	GTEx
rs60229418	RP11-274B21.2	cis	Skin Sun Exposed Lower leg	GTEx
rs60229418	RP11-274B21.4	cis	lung	GTEx
rs60229418	RP11-274B21.2	cis	Stomach	GTEx
rs60229418	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs60229418	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs60229418	RP11-274B21.2	cis	Nerve Tibial	GTEx
rs60229418	RP11-274B21.4	cis	Nerve Tibial	GTEx
rs60229418	RP11-274B21.4	cis	Artery Tibial	GTEx
rs60229418	RP11-274B21.1	cis	Artery Aorta	GTEx
rs60229418	RP11-274B21.4	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128239200-128296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:128249600-128295200	Weak transcription	NH-A	brain
3	chr7:128249600-128297600	Weak transcription	HUVEC	blood vessel
4	chr7:128249600-128308400	Weak transcription	HSMM	muscle
5	chr7:128249600-128312200	Weak transcription	Psoas Muscle	Psoas
6	chr7:128249600-128319600	Weak transcription	NHLF	lung
7	chr7:128260000-128296400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:128260400-128300600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:128272200-128300000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:128274200-128296400	Weak transcription	Colonic Mucosa	Colon
11	chr7:128275600-128295000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:128279600-128296200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr7:128279800-128296400	Weak transcription	Brain Angular Gyrus	brain
14	chr7:128279800-128300000	Weak transcription	Dnd41	blood
15	chr7:128279800-128301400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:128282400-128295400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:128282400-128301400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:128282400-128312400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:128282600-128300000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:128284000-128304800	Weak transcription	Primary T cells from cord blood	blood
21	chr7:128284200-128294600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:128284200-128301400	Weak transcription	Fetal Lung	lung
23	chr7:128284200-128313200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr7:128284400-128299200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:128284400-128313200	Weak transcription	Colon Smooth Muscle	Colon
26	chr7:128285800-128296000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr7:128286400-128298400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr7:128287400-128301400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:128288800-128296200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr7:128289000-128301400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:128290000-128295000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:128290000-128295000	Strong transcription	Liver	Liver
33	chr7:128290000-128295200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr7:128290600-128294600	Strong transcription	Fetal Brain Female	brain
35	chr7:128290600-128295000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr7:128290600-128295000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:128290600-128295000	Strong transcription	Pancreas	Pancrea
38	chr7:128290600-128295400	Strong transcription	Fetal Intestine Small	intestine
39	chr7:128290600-128295800	Strong transcription	Fetal Stomach	stomach
40	chr7:128290800-128294800	Strong transcription	Thymus	Thymus
41	chr7:128290800-128295000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr7:128290800-128295000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr7:128290800-128295000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:128290800-128295000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr7:128291000-128294800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr7:128291000-128295000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr7:128291000-128295000	Strong transcription	Lung	lung
48	chr7:128291200-128294600	Strong transcription	Spleen	Spleen
49	chr7:128291200-128294800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:128291200-128294800	Strong transcription	Gastric	stomach

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