Variant report

Variant	rs9332411
Chromosome Location	chr12:9834345-9834346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1044771	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1056151	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10844427	0.86[ASN][1000 genomes]
rs10844472	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11052372	0.82[CHD][hapmap]
rs11052497	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11052552	0.84[CHD][hapmap]
rs11052582	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12424826	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12427310	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12582584	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1560011	0.90[CHB][hapmap]
rs1985788	0.81[EUR][1000 genomes]
rs2012643	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2080211	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs2098298	0.88[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2114871	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2268146	0.81[CHD][hapmap]
rs2894	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2895988	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3764021	0.84[CHD][hapmap]
rs4763840	0.89[CEU][hapmap]
rs4763879	0.80[ASW][hapmap]
rs61915472	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61915473	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7310460	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7960328	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7974396	0.88[CHB][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7977940	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs917913	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9332411	CLECL1	Cis_1M	lymphoblastoid	RTeQTL
rs9332411	CLECL1	cis	Nerve Tibial	GTEx
rs9332411	CLEC2D	Cis_1M	lymphoblastoid	RTeQTL
rs9332411	CLEC2A	cis	parietal	SCAN
rs9332411	DCAL1	cis	multi-tissue	Pritchard
rs9332411	PHC1	cis	lymphoblastoid	seeQTL
rs9332411	CLEC2D	cis	multi-tissue	Pritchard

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:9815200-9840600	Weak transcription	Fetal Brain Male	brain
4	chr12:9815200-9841600	Weak transcription	Fetal Kidney	kidney
5	chr12:9816200-9840600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:9817200-9837800	Weak transcription	Aorta	Aorta
7	chr12:9818000-9839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:9818000-9839800	Weak transcription	Ovary	ovary
9	chr12:9818000-9840000	Weak transcription	Fetal Intestine Large	intestine
10	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
11	chr12:9818200-9840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:9826400-9849000	Weak transcription	Psoas Muscle	Psoas
13	chr12:9826600-9847200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:9826600-9852400	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:9826800-9837400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:9826800-9840000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:9826800-9840600	Weak transcription	HSMMtube	muscle
18	chr12:9826800-9841000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:9826800-9841400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:9826800-9844600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:9826800-9848400	Weak transcription	Colonic Mucosa	Colon
22	chr12:9826800-9849400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:9826800-9849800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
25	chr12:9827000-9837400	Weak transcription	Right Ventricle	heart
26	chr12:9827000-9840800	Weak transcription	Adipose Nuclei	Adipose
27	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:9827200-9835000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:9827200-9835000	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:9827200-9837600	Weak transcription	Fetal Heart	heart
31	chr12:9827200-9837800	Weak transcription	Fetal Intestine Small	intestine
32	chr12:9827200-9837800	Weak transcription	Fetal Stomach	stomach
33	chr12:9827200-9837800	Weak transcription	Left Ventricle	heart
34	chr12:9827200-9838400	Weak transcription	Spleen	Spleen
35	chr12:9827200-9840200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:9827200-9840600	Weak transcription	HSMM	muscle
37	chr12:9827200-9841000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:9827200-9847000	Weak transcription	NH-A	brain
39	chr12:9827200-9847400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:9827200-9847600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:9827200-9851000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:9827200-9851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:9827200-9852400	Weak transcription	Osteobl	bone
44	chr12:9827400-9840600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:9827400-9849000	Weak transcription	A549	lung
46	chr12:9828400-9835400	ZNF genes & repeats	GM12878-XiMat	blood
47	chr12:9828800-9840600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:9831600-9835800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:9832200-9834400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr12:9832200-9835200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood

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