Variant report

Variant	rs7310460
Chromosome Location	chr12:9840773-9840774
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9798180..9800889-chr12:9840651..9843314,2	K562	blood:
2	chr12:9787751..9790027-chr12:9840631..9842655,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256594	Chromatin interaction
ENSG00000256442	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1008610	0.85[JPT][hapmap]
rs1044771	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]
rs10466829	0.91[JPT][hapmap]
rs10492165	0.85[JPT][hapmap]
rs10492166	0.85[JPT][hapmap]
rs1056151	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743823	0.82[JPT][hapmap]
rs10772046	0.85[ASN][1000 genomes]
rs10772062	0.82[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];0.85[ASN][1000 genomes]
rs10844468	0.85[ASN][1000 genomes]
rs10844472	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844503	0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10844537	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10844562	0.82[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];0.87[ASN][1000 genomes]
rs11052423	0.81[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs11052426	0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11052497	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052552	0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11052582	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11052604	0.84[ASN][1000 genomes]
rs11052710	0.91[JPT][hapmap]
rs11052877	0.85[JPT][hapmap]
rs12227655	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12228641	0.81[ASN][1000 genomes]
rs12424826	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12427310	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12582584	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560011	1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs17806710	0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1985788	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2012643	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2080206	0.93[ASN][1000 genomes]
rs2080211	0.90[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2098298	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2114870	0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2114871	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268146	0.85[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2401391	0.90[JPT][hapmap]
rs2401393	0.91[JPT][hapmap]
rs2894	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895988	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]
rs3764021	0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3764022	0.81[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4763283	0.88[ASN][1000 genomes]
rs4763839	0.87[ASN][1000 genomes]
rs4763840	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4763879	0.80[ASW][hapmap]
rs61915472	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61915473	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7296241	0.90[JPT][hapmap]
rs7306304	0.91[JPT][hapmap]
rs7306557	0.91[JPT][hapmap]
rs741200	0.88[ASN][1000 genomes]
rs7960328	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964018	0.92[ASN][1000 genomes]
rs7968401	0.85[ASN][1000 genomes]
rs7970116	0.91[JPT][hapmap]
rs7973638	0.91[JPT][hapmap]
rs7974396	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977720	0.83[ASN][1000 genomes]
rs7977940	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917911	0.90[JPT][hapmap]
rs917913	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332411	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]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7310460	CLECL1	cis	Nerve Tibial	GTEx
rs7310460	PHC1	cis	lymphoblastoid	seeQTL
rs7310460	CLEC2A	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

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	chr12:9815200-9841600	Weak transcription	Fetal Kidney	kidney
4	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
5	chr12:9826400-9849000	Weak transcription	Psoas Muscle	Psoas
6	chr12:9826600-9847200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:9826600-9852400	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:9826800-9841000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:9826800-9841400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:9826800-9844600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:9826800-9848400	Weak transcription	Colonic Mucosa	Colon
12	chr12:9826800-9849400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:9826800-9849800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
15	chr12:9827000-9840800	Weak transcription	Adipose Nuclei	Adipose
16	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:9827200-9841000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:9827200-9847000	Weak transcription	NH-A	brain
19	chr12:9827200-9847400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:9827200-9847600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:9827200-9851000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:9827200-9851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:9827200-9852400	Weak transcription	Osteobl	bone
24	chr12:9827400-9849000	Weak transcription	A549	lung
25	chr12:9832800-9846000	Weak transcription	Gastric	stomach
26	chr12:9833000-9849000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:9833200-9847200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:9834000-9840800	Weak transcription	Placenta	Placenta
29	chr12:9835400-9849200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:9835800-9847000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:9836000-9843000	Weak transcription	Liver	Liver
32	chr12:9836200-9840800	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr12:9836800-9841800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr12:9837000-9841000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:9837000-9841200	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr12:9837000-9847400	Weak transcription	Fetal Brain Female	brain
37	chr12:9837200-9841800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:9837400-9842000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr12:9837600-9842400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:9837800-9841200	Strong transcription	Thymus	Thymus
41	chr12:9837800-9841800	Strong transcription	Fetal Muscle Leg	muscle
42	chr12:9837800-9842000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:9837800-9846800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr12:9837800-9849400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:9838200-9841400	Weak transcription	Fetal Heart	heart
46	chr12:9838200-9849800	Strong transcription	Fetal Thymus	thymus
47	chr12:9838400-9844800	Weak transcription	Left Ventricle	heart
48	chr12:9838400-9849600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:9838600-9841000	Weak transcription	Right Ventricle	heart
50	chr12:9838600-9841600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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