Variant report

Variant	rs11052497
Chromosome Location	chr12:9849275-9849276
allele	C/T
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: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1044771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1056151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772046	0.85[ASN][1000 genomes]
rs10772062	0.82[ASN][1000 genomes]
rs10844456	0.85[ASN][1000 genomes]
rs10844468	0.85[ASN][1000 genomes]
rs10844472	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844503	0.85[ASN][1000 genomes]
rs10844537	0.84[ASN][1000 genomes]
rs10844562	0.82[ASN][1000 genomes]
rs11052372	0.87[ASN][1000 genomes]
rs11052423	0.85[ASN][1000 genomes]
rs11052426	0.85[ASN][1000 genomes]
rs11052552	0.87[ASN][1000 genomes]
rs11052582	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11052604	0.84[ASN][1000 genomes]
rs12227655	0.82[ASN][1000 genomes]
rs12228641	0.81[ASN][1000 genomes]
rs12424826	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12427310	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12582584	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560011	0.87[ASN][1000 genomes]
rs17806710	0.85[ASN][1000 genomes]
rs1985788	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2012643	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2080206	0.97[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2080211	0.99[ASN][1000 genomes]
rs2098298	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2114870	0.81[ASN][1000 genomes]
rs2114871	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268146	0.80[ASN][1000 genomes]
rs2894	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895988	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764021	0.87[ASN][1000 genomes]
rs3764022	0.85[ASN][1000 genomes]
rs4763283	0.88[ASN][1000 genomes]
rs4763839	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4763840	0.88[ASN][1000 genomes]
rs61915472	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61915473	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7310460	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741200	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7960328	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964018	0.92[ASN][1000 genomes]
rs7968401	0.85[ASN][1000 genomes]
rs7974396	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977720	0.83[ASN][1000 genomes]
rs7977940	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917913	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332411	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11052497	CLEC2D	Cis_1M	lymphoblastoid	RTeQTL
rs11052497	CLECL1	cis	Nerve Tibial	GTEx
rs11052497	CLECL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 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	chr12:9826800-9849400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:9826800-9849800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
7	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:9827200-9851000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:9827200-9851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:9827200-9852400	Weak transcription	Osteobl	bone
11	chr12:9837800-9849400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:9838200-9849800	Strong transcription	Fetal Thymus	thymus
13	chr12:9838400-9849600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:9838800-9854400	Weak transcription	Spleen	Spleen
15	chr12:9839000-9854400	Weak transcription	Lung	lung
16	chr12:9839400-9854600	Weak transcription	Small Intestine	intestine
17	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:9841000-9849600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:9841800-9854800	Weak transcription	Right Ventricle	heart
20	chr12:9841800-9863200	Weak transcription	HSMMtube	muscle
21	chr12:9842200-9850800	Weak transcription	Fetal Brain Male	brain
22	chr12:9842800-9852200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:9843000-9849400	Weak transcription	NHDF-Ad	bronchial
24	chr12:9844000-9852400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:9844200-9860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:9845600-9849600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
27	chr12:9846000-9852400	Weak transcription	NHLF	lung
28	chr12:9846800-9849400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr12:9847400-9849400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:9847600-9849600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
31	chr12:9847600-9850400	Weak transcription	Fetal Heart	heart
32	chr12:9847600-9860000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:9847800-9849400	Weak transcription	NH-A	brain
34	chr12:9847800-9850400	Weak transcription	HSMM	muscle
35	chr12:9847800-9850600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:9848000-9849600	Weak transcription	Placenta	Placenta
37	chr12:9848000-9850000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:9848000-9850800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr12:9848000-9851800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:9848200-9849400	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr12:9848200-9849600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr12:9848200-9850600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:9848200-9852200	Weak transcription	Fetal Lung	lung
44	chr12:9848200-9860200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:9848400-9849800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:9848400-9850200	Weak transcription	Fetal Stomach	stomach
47	chr12:9848400-9850800	Weak transcription	Fetal Kidney	kidney
48	chr12:9848400-9851600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:9848400-9852000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:9848400-9852400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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