Variant report

Variant	rs7299738
Chromosome Location	chr12:9813095-9813096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:9799797..9802431-chr12:9811559..9813864,2	MCF-7	breast:
2	chr12:9811398..9813621-chr12:9843826..9845661,2	MCF-7	breast:
3	chr12:9807912..9810115-chr12:9811259..9815129,3	MCF-7	breast:
4	chr12:9810242..9813132-chr12:9813704..9817912,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLRF1-1	chr12:9812237-9814681	ENSG00000257027.1

Variant related genes	Relation type
ENSG00000256594	Chromatin interaction
ENSG00000256442	Chromatin interaction
ENSG00000069493	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10466762	1.00[ASN][1000 genomes]
rs10772005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772006	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844236	0.89[ASN][1000 genomes]
rs10844267	1.00[ASN][1000 genomes]
rs10844327	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844369	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052207	1.00[ASN][1000 genomes]
rs11052209	1.00[ASN][1000 genomes]
rs11052234	1.00[ASN][1000 genomes]
rs11052235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052254	1.00[ASN][1000 genomes]
rs11052274	0.83[AFR][1000 genomes]
rs11052282	0.89[ASN][1000 genomes]
rs11608817	0.89[ASN][1000 genomes]
rs11830731	0.81[AFR][1000 genomes]
rs12310789	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366653	1.00[ASN][1000 genomes]
rs12366792	1.00[ASN][1000 genomes]
rs12809846	1.00[ASN][1000 genomes]
rs12820641	0.89[ASN][1000 genomes]
rs12830419	0.89[ASN][1000 genomes]
rs12831287	1.00[ASN][1000 genomes]
rs1560008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560010	0.90[AFR][1000 genomes]
rs16913477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863871	1.00[ASN][1000 genomes]
rs2114869	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34323946	0.89[ASN][1000 genomes]
rs34333636	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34833649	1.00[ASN][1000 genomes]
rs34981673	1.00[ASN][1000 genomes]
rs35015427	1.00[ASN][1000 genomes]
rs35098654	1.00[ASN][1000 genomes]
rs35181877	0.89[ASN][1000 genomes]
rs35280686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35561167	1.00[ASN][1000 genomes]
rs35642909	1.00[ASN][1000 genomes]
rs35671537	1.00[ASN][1000 genomes]
rs35884213	1.00[ASN][1000 genomes]
rs55873283	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61916061	0.89[ASN][1000 genomes]
rs6488065	0.89[ASN][1000 genomes]
rs7132037	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136821	0.89[ASN][1000 genomes]
rs7302110	1.00[ASN][1000 genomes]
rs7302746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303246	0.89[ASN][1000 genomes]
rs7304321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305937	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309800	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959406	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959726	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961262	1.00[ASN][1000 genomes]
rs7961416	1.00[ASN][1000 genomes]
rs7962321	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967102	0.89[ASN][1000 genomes]
rs7973603	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974871	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978187	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958340	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919786	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919787	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][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	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7299738	RP11-705C15.2	cis	Whole Blood	GTEx
rs7299738	RP11-705C15.2	cis	Esophagus Mucosa	GTEx
rs7299738	RP11-705C15.3	cis	Whole Blood	GTEx
rs7299738	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9801600-9815600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:9802200-9815200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
4	chr12:9802600-9814400	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:9803000-9816400	Weak transcription	Brain Germinal Matrix	brain
6	chr12:9803000-9816800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:9803000-9819800	Weak transcription	Fetal Brain Female	brain
8	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
9	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
10	chr12:9803200-9813400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
12	chr12:9804000-9814200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:9804200-9813200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:9804200-9814200	Weak transcription	Colonic Mucosa	Colon
15	chr12:9804200-9814600	Weak transcription	Lung	lung
16	chr12:9804200-9815000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:9804400-9814600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:9804400-9820400	Weak transcription	HUVEC	blood vessel
19	chr12:9804600-9820000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:9804600-9820000	Weak transcription	HMEC	breast
21	chr12:9804600-9820200	Weak transcription	NHEK	skin
22	chr12:9805000-9813800	Weak transcription	K562	blood
23	chr12:9805600-9813600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
24	chr12:9805600-9815000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:9805600-9819400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:9805800-9818200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:9806000-9813400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:9806000-9813400	Weak transcription	Fetal Brain Male	brain
29	chr12:9806000-9814400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:9806000-9814800	Strong transcription	Fetal Thymus	thymus
31	chr12:9806000-9815400	Strong transcription	Fetal Intestine Large	intestine
32	chr12:9806000-9818000	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:9806200-9814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:9806200-9815800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr12:9806200-9818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:9806200-9818200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:9806200-9819000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr12:9806200-9821600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr12:9806400-9813200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:9806400-9814400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:9806400-9815200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:9806400-9815800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:9806400-9816000	Strong transcription	Osteobl	bone
44	chr12:9806400-9817200	Strong transcription	Dnd41	blood
45	chr12:9806600-9815400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:9806600-9818000	Strong transcription	Placenta	Placenta
47	chr12:9806600-9818600	Strong transcription	Adipose Nuclei	Adipose
48	chr12:9806600-9818600	Strong transcription	Fetal Lung	lung
49	chr12:9807000-9815000	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr12:9807000-9818000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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