Variant report

Variant	rs12694860
Chromosome Location	chr2:231267157-231267158
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231263713..231265623-chr2:231266968..231269149,2	K562	blood:

Variant related genes	Relation type
ENSG00000185404	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10165727	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10181582	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10181779	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10184953	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10189380	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10194531	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10198517	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11686704	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12694850	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12694851	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12694853	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12694854	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12694855	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12694856	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12694858	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12694859	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12694862	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694863	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12994857	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13012177	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13012615	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13025664	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13028885	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13383901	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13383916	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13383946	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13384148	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13384237	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13384350	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13390006	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13397699	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13409103	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1579395	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1609427	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1820551	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1863672	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1968342	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2894710	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35935297	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856528	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4364013	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577270	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4638786	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6709797	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6710190	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6738146	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6738151	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7585740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7586155	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9288667	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv875945	chr2:231172642-231267925	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv869708	chr2:231173700-231267616	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1006206	chr2:231179884-231268938	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv875946	chr2:231184106-231277567	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv979180	chr2:231264860-231267173	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12694860	LOC93349	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231220000-231275800	Weak transcription	Stomach Mucosa	stomach
2	chr2:231222200-231273200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:231225200-231268000	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:231228800-231275600	Weak transcription	Psoas Muscle	Psoas
5	chr2:231234200-231274400	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:231248000-231274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:231249000-231273200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:231250200-231273200	Weak transcription	Right Ventricle	heart
9	chr2:231252600-231272600	Weak transcription	NHDF-Ad	bronchial
10	chr2:231254200-231272800	Weak transcription	NHEK	skin
11	chr2:231254400-231267800	Weak transcription	NHLF	lung
12	chr2:231255200-231275600	Weak transcription	HMEC	breast
13	chr2:231258000-231267600	Weak transcription	Esophagus	oesophagus
14	chr2:231258200-231273000	Weak transcription	NH-A	brain
15	chr2:231258800-231275600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:231259600-231268200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:231260200-231275400	Weak transcription	Small Intestine	intestine
18	chr2:231260800-231272000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:231261000-231268400	Weak transcription	Fetal Lung	lung
20	chr2:231261000-231270600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:231261000-231271400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:231261000-231271400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:231261000-231271800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:231261000-231272000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:231261200-231271800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:231262200-231267400	Weak transcription	Osteobl	bone
27	chr2:231262200-231268200	Weak transcription	Left Ventricle	heart
28	chr2:231262800-231267400	Weak transcription	GM12878-XiMat	blood
29	chr2:231262800-231273200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:231263600-231268000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:231264000-231270600	Strong transcription	Liver	Liver
32	chr2:231264600-231275800	Weak transcription	K562	blood
33	chr2:231265000-231267400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:231265000-231275600	Weak transcription	Fetal Heart	heart
35	chr2:231265200-231272800	Weak transcription	HSMM	muscle
36	chr2:231265200-231273000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr2:231265400-231267200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:231265400-231267400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:231265400-231270200	Weak transcription	HSMMtube	muscle
40	chr2:231265400-231272800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:231265400-231275400	Weak transcription	HepG2	liver
42	chr2:231265600-231267200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:231265600-231267200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:231265600-231267200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:231265600-231267200	Weak transcription	Dnd41	blood
46	chr2:231265600-231267400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:231265600-231267400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:231265600-231267400	Weak transcription	Fetal Thymus	thymus
49	chr2:231265600-231267400	Weak transcription	Spleen	Spleen
50	chr2:231265600-231267600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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