Variant report

Variant	rs1044771
Chromosome Location	chr12:9851929-9851930
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:9849159-9855177	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:9850844-9851975	GM12891	blood:	n/a	n/a
3	MTA3	chr12:9851111-9851951	GM12878	blood:	n/a	n/a
4	CEBPB	chr12:9851924-9852196	HepG2	liver:	n/a	chr12:9852073-9852084 chr12:9852073-9852082 chr12:9852071-9852082 chr12:9852071-9852084
5	POLR2A	chr12:9850863-9852020	GM12892	blood:	n/a	n/a
6	CEBPB	chr12:9851913-9852207	A549	lung:	n/a	chr12:9852073-9852084 chr12:9852073-9852082 chr12:9852071-9852082 chr12:9852071-9852084
7	POLR2A	chr12:9851235-9851992	GM12878	blood:	n/a	n/a
8	CEBPB	chr12:9851898-9852261	IMR90	lung:	n/a	chr12:9852073-9852084 chr12:9852202-9852210 chr12:9852073-9852082 chr12:9852071-9852082 chr12:9852071-9852084
9	REST	chr12:9851876-9853227	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9851492..9853618-chr12:9859229..9860813,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000256582	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1008610	0.85[JPT][hapmap]
rs10466829	0.91[JPT][hapmap]
rs10492165	0.85[JPT][hapmap]
rs10492166	0.85[JPT][hapmap]
rs1056151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10743823	0.82[JPT][hapmap]
rs10772046	0.84[ASN][1000 genomes]
rs10772062	0.81[ASN][1000 genomes]
rs10772085	0.91[JPT][hapmap]
rs10772087	0.85[JPT][hapmap]
rs10772102	0.85[JPT][hapmap]
rs10844456	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10844468	0.84[ASN][1000 genomes]
rs10844472	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10844503	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10844537	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10844562	0.81[ASN][1000 genomes]
rs10844615	0.91[JPT][hapmap]
rs10844617	0.91[JPT][hapmap]
rs10844620	0.84[JPT][hapmap]
rs10844636	0.85[JPT][hapmap]
rs10844638	0.85[JPT][hapmap]
rs10844657	0.85[JPT][hapmap]
rs11052372	0.81[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11052423	0.81[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11052426	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11052497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11052552	0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[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	0.83[ASN][1000 genomes]
rs11052710	0.91[JPT][hapmap]
rs11052877	0.85[JPT][hapmap]
rs12227655	0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12228641	0.80[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];0.97[ASN][1000 genomes]
rs1560011	1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs17806710	0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[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	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2098298	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2114870	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2114871	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2268146	0.85[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
rs2401391	0.90[JPT][hapmap]
rs2401393	0.91[JPT][hapmap]
rs2894	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2895988	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]
rs3764021	0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3764022	0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4763283	0.88[ASN][1000 genomes]
rs4763839	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4763840	0.89[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4763879	0.80[ASW][hapmap];0.83[MEX][hapmap];0.87[YRI][hapmap]
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]
rs7296241	0.90[JPT][hapmap]
rs7306304	0.91[JPT][hapmap]
rs7306557	0.91[JPT][hapmap]
rs7310460	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	0.83[ASN][1000 genomes]
rs7970116	0.91[JPT][hapmap]
rs7973638	0.91[JPT][hapmap]
rs7974396	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977720	0.82[ASN][1000 genomes]
rs7977940	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs917911	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs917913	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332411	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]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1044771	CLEC2A	cis	parietal	SCAN
rs1044771	PHC1	cis	lymphoblastoid	seeQTL
rs1044771	CLEC2D	Cis_1M	lymphoblastoid	RTeQTL
rs1044771	CLECL1	cis	Nerve Tibial	GTEx
rs1044771	CLECL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9826600-9852400	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
3	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:9827200-9852400	Weak transcription	Osteobl	bone
5	chr12:9838800-9854400	Weak transcription	Spleen	Spleen
6	chr12:9839000-9854400	Weak transcription	Lung	lung
7	chr12:9839400-9854600	Weak transcription	Small Intestine	intestine
8	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:9841800-9854800	Weak transcription	Right Ventricle	heart
10	chr12:9841800-9863200	Weak transcription	HSMMtube	muscle
11	chr12:9842800-9852200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:9844000-9852400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:9844200-9860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:9846000-9852400	Weak transcription	NHLF	lung
15	chr12:9847600-9860000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:9848200-9852200	Weak transcription	Fetal Lung	lung
17	chr12:9848200-9860200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:9848400-9852000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:9848400-9852400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:9848400-9853000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:9848400-9854000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:9848400-9860200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:9848600-9859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:9849400-9852000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:9849400-9853000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:9849400-9853200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:9849400-9854000	Weak transcription	Thymus	Thymus
28	chr12:9849600-9852200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:9849800-9853200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr12:9849800-9854000	Weak transcription	Fetal Thymus	thymus
31	chr12:9849800-9860600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:9850000-9854400	Weak transcription	Left Ventricle	heart
33	chr12:9850200-9854200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:9850400-9852400	Enhancers	Fetal Heart	heart
35	chr12:9850400-9854400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:9850400-9854600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:9850800-9853400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr12:9851000-9852400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:9851000-9853400	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr12:9851200-9852200	Enhancers	Primary B cells from cord blood	blood
41	chr12:9851200-9852800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr12:9851200-9854600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr12:9851400-9852200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr12:9851400-9853200	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr12:9851400-9853200	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr12:9851400-9854400	Enhancers	Primary T cells from cord blood	blood
47	chr12:9851600-9852600	Weak transcription	Dnd41	blood
48	chr12:9851600-9852800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:9851600-9852800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:9851800-9852600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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