Variant report

Variant	rs12617669
Chromosome Location	chr2:152139787-152139788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152124159..152126726-chr2:152137023..152139855,2	K562	blood:
2	chr2:152137402..152140288-chr2:152140945..152142513,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10169816	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176271	0.82[EUR][1000 genomes]
rs10182245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187344	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11679466	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617724	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278089	0.88[EUR][1000 genomes]
rs2880489	0.80[EUR][1000 genomes]
rs289828	0.88[EUR][1000 genomes]
rs289829	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289832	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289833	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289835	0.86[EUR][1000 genomes]
rs35058039	0.80[EUR][1000 genomes]
rs35499578	0.88[EUR][1000 genomes]
rs3771886	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771887	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771888	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387297	0.85[EUR][1000 genomes]
rs4664357	0.80[EUR][1000 genomes]
rs4665159	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715393	0.87[EUR][1000 genomes]
rs6718415	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747782	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751802	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6757821	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523849	chr2:151718133-152143524	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
10	esv1793984	chr2:152138749-152154163	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12617669	NMI	Cis_1M	lymphoblastoid	RTeQTL
rs12617669	TNFAIP6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152118600-152142800	Weak transcription	Small Intestine	intestine
2	chr2:152118800-152144000	Weak transcription	Stomach Mucosa	stomach
3	chr2:152118800-152144200	Weak transcription	Psoas Muscle	Psoas
4	chr2:152119000-152145000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:152119000-152145200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:152119000-152145200	Weak transcription	NHEK	skin
7	chr2:152119000-152145800	Weak transcription	HSMM	muscle
8	chr2:152119400-152142800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:152119400-152144400	Weak transcription	A549	lung
10	chr2:152119400-152144800	Weak transcription	Brain Substantia Nigra	brain
11	chr2:152119400-152145200	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:152121200-152145000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:152121200-152145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:152125200-152145400	Weak transcription	Aorta	Aorta
15	chr2:152125800-152145200	Weak transcription	Right Ventricle	heart
16	chr2:152126200-152139800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:152126200-152141200	Strong transcription	Dnd41	blood
18	chr2:152126800-152145200	Weak transcription	HMEC	breast
19	chr2:152126800-152145600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:152127000-152145400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:152128000-152144600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:152128400-152145200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:152128600-152145200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:152130200-152145600	Weak transcription	Fetal Kidney	kidney
25	chr2:152130600-152144600	Weak transcription	Fetal Lung	lung
26	chr2:152134400-152144800	Weak transcription	Esophagus	oesophagus
27	chr2:152134400-152145200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:152134400-152145400	Weak transcription	Gastric	stomach
29	chr2:152134800-152144800	Weak transcription	Fetal Stomach	stomach
30	chr2:152134800-152144800	Weak transcription	Pancreas	Pancrea
31	chr2:152134800-152144800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:152134800-152145000	Weak transcription	Colonic Mucosa	Colon
33	chr2:152135000-152144600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:152135000-152144800	Weak transcription	Lung	lung
35	chr2:152135000-152145200	Weak transcription	NHLF	lung
36	chr2:152135200-152144800	Weak transcription	Left Ventricle	heart
37	chr2:152135400-152143000	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:152135400-152144800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:152135400-152145200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:152136600-152145200	Weak transcription	NH-A	brain
41	chr2:152136800-152144200	Weak transcription	HUVEC	blood vessel
42	chr2:152137200-152145400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:152137400-152144800	Weak transcription	Osteobl	bone
44	chr2:152137400-152145200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:152137600-152142800	Weak transcription	Spleen	Spleen
46	chr2:152137800-152142000	Weak transcription	Fetal Intestine Small	intestine
47	chr2:152138000-152140200	Strong transcription	GM12878-XiMat	blood
48	chr2:152138600-152144200	Weak transcription	Hela-S3	cervix
49	chr2:152139000-152142600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:152139000-152144600	Weak transcription	Brain Anterior Caudate	brain

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