Variant report

Variant	rs1234354
Chromosome Location	chr7:150385900-150385901
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	chr7:150384449..150386247-chr7:150390461..150392753,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10241142	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10245231	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10250584	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10260218	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10265803	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1234353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234358	0.91[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1234359	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1234362	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1234363	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12703092	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17173566	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2049247	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2049249	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2140144	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2373844	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3936752	0.90[EUR][1000 genomes]
rs6946579	0.84[TSI][hapmap]
rs6962505	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6965369	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6976084	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1234354	DPP6	cis	parietal	SCAN
rs1234354	GIMAP8	Cis_1M	lymphoblastoid	RTeQTL
rs1234354	HCA112	cis	multi-tissue	Pritchard
rs1234354	LR8	cis	multi-tissue	Pritchard
rs1234354	MAFF	trans	multi-tissue	Pritchard
rs1234354	GIMAP4	Cis_1M	lymphoblastoid	RTeQTL
rs1234354	GIMAP4	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150383400-150387600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr7:150383400-150388400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:150383600-150386200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:150383600-150387200	Weak transcription	Placenta	Placenta
5	chr7:150383600-150389400	Weak transcription	Fetal Stomach	stomach
6	chr7:150383600-150389600	Weak transcription	Fetal Muscle Leg	muscle
7	chr7:150383600-150390800	Weak transcription	Small Intestine	intestine
8	chr7:150383600-150391000	Weak transcription	Gastric	stomach
9	chr7:150383600-150391400	Weak transcription	Brain Substantia Nigra	brain
10	chr7:150383800-150386000	Weak transcription	Fetal Intestine Small	intestine
11	chr7:150383800-150387200	Weak transcription	Colonic Mucosa	Colon
12	chr7:150383800-150387200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:150383800-150387200	Weak transcription	Fetal Lung	lung
14	chr7:150383800-150387200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:150383800-150392200	Weak transcription	Right Atrium	heart
16	chr7:150383800-150392200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr7:150384200-150390600	ZNF genes & repeats	GM12878-XiMat	blood
18	chr7:150384600-150388800	Genic enhancers	Spleen	Spleen
19	chr7:150384800-150386000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
20	chr7:150384800-150386600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
21	chr7:150384800-150387000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr7:150384800-150387000	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
23	chr7:150384800-150388200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
24	chr7:150385000-150386600	Genic enhancers	Thymus	Thymus
25	chr7:150385000-150387000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
26	chr7:150385000-150387200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
27	chr7:150385000-150391600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr7:150385200-150386000	Enhancers	Adipose Nuclei	Adipose
29	chr7:150385200-150386400	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
30	chr7:150385200-150387200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr7:150385200-150388000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr7:150385200-150388400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr7:150385200-150390400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:150385200-150390400	Weak transcription	HUVEC	blood vessel
35	chr7:150385400-150386000	Enhancers	Right Ventricle	heart
36	chr7:150385400-150387600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:150385600-150386000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr7:150385600-150386000	Weak transcription	Liver	Liver
39	chr7:150385600-150386000	Enhancers	Esophagus	oesophagus
40	chr7:150385600-150386000	Enhancers	Left Ventricle	heart
41	chr7:150385600-150386200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:150385600-150386200	Enhancers	Lung	lung
43	chr7:150385600-150386600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
44	chr7:150385600-150386800	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr7:150385600-150386800	ZNF genes & repeats	Fetal Thymus	thymus
46	chr7:150385600-150387000	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:150385600-150387600	Strong transcription	Primary B cells from cord blood	blood
48	chr7:150385600-150388600	Strong transcription	Ovary	ovary
49	chr7:150385600-150390000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:150385600-150390000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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