Variant report

Variant	rs11973400
Chromosome Location	chr7:150437087-150437088
allele	C/T
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	CEBPB	chr7:150437073-150437439	Hela-S3	cervix:	n/a	chr7:150437212-150437223 chr7:150437256-150437267
2	FOS	chr7:150437059-150437374	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr7:150437086-150437426	HepG2	liver:	n/a	chr7:150437212-150437223 chr7:150437256-150437267
4	FOS	chr7:150437065-150437442	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr7:150437020-150437331	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr7:150437028-150437303	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150433868..150435484-chr7:150436619..150439022,2	MCF-7	breast:

Variant related genes	Relation type
GIMAP5	TF binding region
ENSG00000196329	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10280499	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11769454	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17173583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58313703	1.00[ASN][1000 genomes]
rs58803836	1.00[ASN][1000 genomes]
rs59004814	1.00[ASN][1000 genomes]
rs66743416	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965571	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741069	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657886	0.86[YRI][hapmap]

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
rs11973400	GIMAP5	cis	normal skin	skin_eQTL
rs11973400	CHPF2	cis	cerebellum	SCAN
rs11973400	ATP6V0E2	cis	parietal	SCAN
rs11973400	GIMAP7	cis	parietal	SCAN
rs11973400	TMEM176A	cis	Whole Blood	GTEx
rs11973400	GIMAP4	cis	parietal	SCAN
rs11973400	TMEM176B	cis	Whole Blood	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150433800-150439200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr7:150434000-150437200	Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr7:150434000-150437400	Active TSS	Brain Anterior Caudate	brain
4	chr7:150434000-150437400	Active TSS	Colonic Mucosa	Colon
5	chr7:150434000-150437600	Active TSS	Lung	lung
6	chr7:150434000-150437600	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr7:150434000-150437600	Active TSS	Right Ventricle	heart
8	chr7:150434000-150437800	Active TSS	Rectal Smooth Muscle	rectum
9	chr7:150434000-150438000	Active TSS	Right Atrium	heart
10	chr7:150434200-150437200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:150434200-150437200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr7:150434200-150437400	Active TSS	Primary T cells fromperipheralblood	blood
13	chr7:150434200-150437600	Active TSS	Brain Hippocampus Middle	brain
14	chr7:150434200-150437600	Active TSS	Left Ventricle	heart
15	chr7:150434200-150437600	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr7:150434200-150437800	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr7:150434200-150437800	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr7:150434200-150438000	Active TSS	Duodenum Mucosa	Duodenum
19	chr7:150434200-150438000	Active TSS	Psoas Muscle	Psoas
20	chr7:150434400-150437200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr7:150434400-150437200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:150434400-150437400	Active TSS	Brain Angular Gyrus	brain
23	chr7:150434400-150437400	Active TSS	Thymus	Thymus
24	chr7:150434400-150437800	Active TSS	Adipose Nuclei	Adipose
25	chr7:150434600-150440600	Transcr. at gene 5' and 3'	Dnd41	blood
26	chr7:150434800-150437400	Active TSS	Primary B cells from cord blood	blood
27	chr7:150434800-150437400	Enhancers	HMEC	breast
28	chr7:150435000-150437800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr7:150435200-150437600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr7:150435200-150437600	Active TSS	Stomach Smooth Muscle	stomach
31	chr7:150435400-150437400	Flanking Active TSS	Liver	Liver
32	chr7:150435400-150437600	Active TSS	Fetal Muscle Leg	muscle
33	chr7:150435400-150439000	Active TSS	GM12878-XiMat	blood
34	chr7:150435400-150442800	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
35	chr7:150435600-150437600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr7:150435600-150442400	Weak transcription	Ovary	ovary
37	chr7:150435800-150437200	Weak transcription	Spleen	Spleen
38	chr7:150435800-150437800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr7:150435800-150439600	Weak transcription	Colon Smooth Muscle	Colon
40	chr7:150435800-150441000	Weak transcription	Pancreas	Pancrea
41	chr7:150435800-150441200	Weak transcription	Gastric	stomach
42	chr7:150435800-150441800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
43	chr7:150436000-150437200	Weak transcription	Esophagus	oesophagus
44	chr7:150436000-150437200	Active TSS	Fetal Thymus	thymus
45	chr7:150436000-150441800	Weak transcription	Fetal Intestine Small	intestine
46	chr7:150436200-150437200	Weak transcription	Small Intestine	intestine
47	chr7:150436200-150437400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr7:150436200-150439600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:150436200-150450200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr7:150436400-150437200	Weak transcription	Fetal Stomach	stomach

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