Variant report

Variant	rs12666485
Chromosome Location	chr7:65625122-65625123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65617048..65619822-chr7:65625013..65626809,2	MCF-7	breast:
2	chr7:65625074..65627224-chr7:65631943..65634316,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10950024	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10950025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10950027	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10950028	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10950029	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11760805	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767833	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12671834	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673308	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs160636	0.82[ASN][1000 genomes]
rs160640	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs160641	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs160645	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs160647	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17138089	0.89[ASN][1000 genomes]
rs17138149	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs221986	0.90[ASN][1000 genomes]
rs2451953	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2460427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465121	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28815324	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2946580	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs313817	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs313818	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313823	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313828	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs313830	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs316305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs316306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs316316	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316320	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs316323	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316328	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400767	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4441996	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4718325	0.86[ASN][1000 genomes]
rs6460276	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6460281	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67302640	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67397473	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67688847	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67775320	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6960870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136346	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73142233	0.86[ASN][1000 genomes]
rs73142245	0.86[ASN][1000 genomes]
rs73376394	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73376401	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73378304	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7782212	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7783727	0.81[ASN][1000 genomes]
rs7786728	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7786735	0.85[ASN][1000 genomes]
rs7787063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	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
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv971172	chr7:65616238-65653268	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12666485	RNU6-96P	cis	Thyroid	GTEx
rs12666485	GS1-124K5.4	cis	Stomach	GTEx
rs12666485	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs12666485	GS1-124K5.11	cis	Thyroid	GTEx
rs12666485	GTF2IRD1P1	cis	Thyroid	GTEx
rs12666485	GS1-124K5.4	cis	Artery Aorta	GTEx
rs12666485	GS1-124K5.4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65612000-65635400	Weak transcription	Fetal Kidney	kidney
2	chr7:65617600-65628800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:65617600-65632400	Weak transcription	Hela-S3	cervix
4	chr7:65618200-65625200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:65618200-65632400	Weak transcription	HUVEC	blood vessel
6	chr7:65618200-65635400	Weak transcription	Esophagus	oesophagus
7	chr7:65618200-65635600	Weak transcription	Right Ventricle	heart
8	chr7:65618800-65625400	Weak transcription	Fetal Heart	heart
9	chr7:65618800-65627600	Weak transcription	NHEK	skin
10	chr7:65619000-65625200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:65619000-65625400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr7:65619000-65627800	Weak transcription	HepG2	liver
13	chr7:65619000-65631200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:65619000-65632400	Weak transcription	NHLF	lung
15	chr7:65619000-65632800	Weak transcription	Gastric	stomach
16	chr7:65619000-65635200	Weak transcription	Spleen	Spleen
17	chr7:65619000-65635400	Weak transcription	Pancreas	Pancrea
18	chr7:65619000-65635600	Weak transcription	HMEC	breast
19	chr7:65619000-65635800	Weak transcription	Colon Smooth Muscle	Colon
20	chr7:65619400-65625400	Weak transcription	Small Intestine	intestine
21	chr7:65619400-65632400	Weak transcription	NHDF-Ad	bronchial
22	chr7:65620800-65635400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:65621000-65625200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:65621000-65627800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:65621200-65625800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr7:65622400-65632800	Weak transcription	Brain Substantia Nigra	brain
27	chr7:65622600-65625200	ZNF genes & repeats	Fetal Stomach	stomach
28	chr7:65622600-65625400	ZNF genes & repeats	Fetal Brain Female	brain
29	chr7:65622600-65635600	Weak transcription	Stomach Mucosa	stomach
30	chr7:65622800-65632600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:65623000-65625600	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr7:65623000-65625800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:65623600-65625200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:65623600-65625200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr7:65623600-65625600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr7:65623600-65626400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:65623600-65627000	Weak transcription	Primary B cells from cord blood	blood
38	chr7:65623600-65627200	Weak transcription	Brain Hippocampus Middle	brain
39	chr7:65623600-65627800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:65623600-65630400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:65623600-65632400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:65623600-65633000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr7:65623600-65635400	Weak transcription	Colonic Mucosa	Colon
44	chr7:65623600-65635600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:65623800-65625200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:65623800-65625200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr7:65623800-65625400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr7:65623800-65625400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr7:65623800-65625400	Weak transcription	Brain Anterior Caudate	brain
50	chr7:65623800-65625400	Weak transcription	Rectal Mucosa Donor 29	rectum

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