Variant report

Variant	rs7979758
Chromosome Location	chr12:9849548-9849549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLRF1-2	chr12:9847356-9852151	NR_036693

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1008611	0.84[ASN][1000 genomes]
rs10743821	0.84[ASN][1000 genomes]
rs10743822	0.84[ASN][1000 genomes]
rs10844418	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844424	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844429	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844449	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844457	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844476	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052303	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11052304	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11052305	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052311	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052327	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052342	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052366	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052367	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052430	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052431	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052434	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052718	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11052785	0.84[ASN][1000 genomes]
rs11519377	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11524523	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12309762	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12320830	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578698	0.84[ASN][1000 genomes]
rs12578928	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582616	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12810851	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817365	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12823699	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825507	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828602	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831453	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990533	0.84[ASN][1000 genomes]
rs2114872	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114873	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192433	0.84[ASN][1000 genomes]
rs2192434	0.84[ASN][1000 genomes]
rs2192435	0.84[ASN][1000 genomes]
rs2192439	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2401396	0.84[ASN][1000 genomes]
rs34201389	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35210729	0.93[AMR][1000 genomes]
rs35237063	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763264	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763835	0.84[ASN][1000 genomes]
rs61913428	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6488109	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6488122	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310897	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954062	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7969074	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7972035	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9630264	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630265	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668568	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs982511	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv975446	chr12:9847906-9852218	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7979758	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
3	chr12:9826600-9852400	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:9826800-9849800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
6	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:9827200-9851000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:9827200-9851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:9827200-9852400	Weak transcription	Osteobl	bone
10	chr12:9838200-9849800	Strong transcription	Fetal Thymus	thymus
11	chr12:9838400-9849600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:9838800-9854400	Weak transcription	Spleen	Spleen
13	chr12:9839000-9854400	Weak transcription	Lung	lung
14	chr12:9839400-9854600	Weak transcription	Small Intestine	intestine
15	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:9841000-9849600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:9841800-9854800	Weak transcription	Right Ventricle	heart
18	chr12:9841800-9863200	Weak transcription	HSMMtube	muscle
19	chr12:9842200-9850800	Weak transcription	Fetal Brain Male	brain
20	chr12:9842800-9852200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr12:9844000-9852400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr12:9844200-9860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:9845600-9849600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
24	chr12:9846000-9852400	Weak transcription	NHLF	lung
25	chr12:9847600-9849600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
26	chr12:9847600-9850400	Weak transcription	Fetal Heart	heart
27	chr12:9847600-9860000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:9847800-9850400	Weak transcription	HSMM	muscle
29	chr12:9847800-9850600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:9848000-9849600	Weak transcription	Placenta	Placenta
31	chr12:9848000-9850000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:9848000-9850800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr12:9848000-9851800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:9848200-9849600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr12:9848200-9850600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:9848200-9852200	Weak transcription	Fetal Lung	lung
37	chr12:9848200-9860200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:9848400-9849800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:9848400-9850200	Weak transcription	Fetal Stomach	stomach
40	chr12:9848400-9850800	Weak transcription	Fetal Kidney	kidney
41	chr12:9848400-9851600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:9848400-9852000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:9848400-9852400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:9848400-9853000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:9848400-9854000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:9848400-9860200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr12:9848600-9849600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr12:9848600-9851000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:9848600-9859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:9848800-9849600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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