Variant report

Variant	rs2895988
Chromosome Location	chr12:9828427-9828428
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1044771	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10466829	0.85[JPT][hapmap]
rs1056151	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772046	0.85[ASN][1000 genomes]
rs10772062	0.82[ASN][1000 genomes]
rs10772085	0.85[JPT][hapmap]
rs10844456	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10844468	0.85[ASN][1000 genomes]
rs10844472	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844503	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10844537	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10844562	0.82[ASN][1000 genomes]
rs10844615	0.85[JPT][hapmap]
rs10844617	0.85[JPT][hapmap]
rs11052372	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11052423	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11052426	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11052497	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052552	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11052582	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11052604	0.84[ASN][1000 genomes]
rs11052710	0.85[JPT][hapmap]
rs12227655	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12228641	0.81[ASN][1000 genomes]
rs12424826	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12427310	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12582584	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560011	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17806710	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1985788	0.89[ASN][1000 genomes]
rs2012643	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2080206	0.93[ASN][1000 genomes]
rs2080211	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2098298	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2114870	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2114871	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268146	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2401391	0.84[JPT][hapmap]
rs2401393	0.85[JPT][hapmap]
rs2894	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764021	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3764022	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4763283	0.88[ASN][1000 genomes]
rs4763839	0.87[ASN][1000 genomes]
rs4763840	0.89[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs61915472	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61915473	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7296241	0.84[JPT][hapmap]
rs7306304	0.85[JPT][hapmap]
rs7306557	0.85[JPT][hapmap]
rs7310460	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741200	0.88[ASN][1000 genomes]
rs7960328	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964018	0.92[ASN][1000 genomes]
rs7968401	0.85[ASN][1000 genomes]
rs7970116	0.85[JPT][hapmap]
rs7973638	0.85[JPT][hapmap]
rs7974396	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977720	0.83[ASN][1000 genomes]
rs7977940	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917911	0.85[JPT][hapmap]
rs917913	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332411	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]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2895988	CLECL1	Cis_1M	lymphoblastoid	RTeQTL
rs2895988	CLECL1	cis	Nerve Tibial	GTEx
rs2895988	CLEC2D	Cis_1M	lymphoblastoid	RTeQTL

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	chr12:9815600-9833800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:9816200-9832600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:9816200-9840600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:9817200-9837800	Weak transcription	Aorta	Aorta
9	chr12:9818000-9839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:9818000-9839800	Weak transcription	Ovary	ovary
11	chr12:9818000-9840000	Weak transcription	Fetal Intestine Large	intestine
12	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
13	chr12:9818200-9828600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:9818200-9840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:9823000-9829800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
16	chr12:9824400-9832600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:9826400-9849000	Weak transcription	Psoas Muscle	Psoas
18	chr12:9826600-9847200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:9826600-9852400	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:9826800-9828600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr12:9826800-9832200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr12:9826800-9833400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:9826800-9833800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:9826800-9837400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:9826800-9840000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:9826800-9840600	Weak transcription	HSMMtube	muscle
27	chr12:9826800-9841000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:9826800-9841400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:9826800-9844600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:9826800-9848400	Weak transcription	Colonic Mucosa	Colon
31	chr12:9826800-9849400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:9826800-9849800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
34	chr12:9827000-9832200	Weak transcription	Placenta	Placenta
35	chr12:9827000-9832600	Weak transcription	Fetal Lung	lung
36	chr12:9827000-9837400	Weak transcription	Right Ventricle	heart
37	chr12:9827000-9840800	Weak transcription	Adipose Nuclei	Adipose
38	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr12:9827200-9828600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:9827200-9828800	Active TSS	Primary T cells fromperipheralblood	blood
41	chr12:9827200-9829600	Weak transcription	HUVEC	blood vessel
42	chr12:9827200-9830400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:9827200-9830400	Weak transcription	Small Intestine	intestine
44	chr12:9827200-9830400	Weak transcription	Thymus	Thymus
45	chr12:9827200-9830800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:9827200-9832400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:9827200-9832400	Weak transcription	Fetal Thymus	thymus
48	chr12:9827200-9832400	Weak transcription	K562	blood
49	chr12:9827200-9832600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:9827200-9832600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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