Variant report

Variant	rs58235667
Chromosome Location	chr7:4031865-4031866
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	chr7:3961683..3962198-chr7:4031551..4032127,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXK1-4	chr7:4029593-4032608	NONHSAT118857

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10250009	1.00[EUR][1000 genomes]
rs11971958	0.84[AMR][1000 genomes]
rs11972874	0.84[AMR][1000 genomes]
rs11973168	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11980257	0.84[AMR][1000 genomes]
rs11983307	0.92[AMR][1000 genomes]
rs11983733	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17134194	1.00[EUR][1000 genomes]
rs59246023	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs73673207	0.84[AMR][1000 genomes]
rs73673212	1.00[EUR][1000 genomes]
rs73673216	0.84[AMR][1000 genomes]
rs73673218	0.84[AMR][1000 genomes]
rs73673219	0.84[AMR][1000 genomes]
rs750293	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1025497	chr7:3905444-4176032	Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv538686	chr7:3905444-4176032	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv433014	chr7:3910039-4054769	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv464274	chr7:3955516-4613607	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv464275	chr7:3955516-4613607	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv464276	chr7:3955516-4613607	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv464277	chr7:3955516-4613607	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv464278	chr7:3955516-4613607	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv605939	chr7:3955516-4613607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1019086	chr7:3968656-4044519	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv538687	chr7:3968656-4044519	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1019305	chr7:3991646-4276004	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv1033687	chr7:4006020-4267871	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv538688	chr7:4006020-4267871	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv917252	chr7:4017819-4374090	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv527624	chr7:4027536-4424054	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58235667	TAP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3988600-4032600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr7:3996400-4037600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:3998400-4045600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:4000200-4032600	Weak transcription	Adipose Nuclei	Adipose
5	chr7:4015600-4036200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:4019200-4045800	Weak transcription	Fetal Brain Female	brain
7	chr7:4022000-4041200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:4022000-4057800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:4022200-4046000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:4024000-4037200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:4027000-4033400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:4027400-4035200	Weak transcription	Fetal Lung	lung
13	chr7:4029000-4034600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:4030600-4046000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:4030600-4046400	Weak transcription	Fetal Intestine Small	intestine
16	chr7:4030800-4032200	Enhancers	Fetal Muscle Trunk	muscle
17	chr7:4030800-4032400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr7:4030800-4032600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:4030800-4033000	Enhancers	Fetal Muscle Leg	muscle
20	chr7:4031000-4032000	Enhancers	Brain Germinal Matrix	brain
21	chr7:4031000-4050000	Weak transcription	Pancreas	Pancrea
22	chr7:4031200-4032000	Enhancers	Psoas Muscle	Psoas
23	chr7:4031200-4032000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr7:4031200-4037400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:4031200-4038200	Weak transcription	HSMMtube	muscle
26	chr7:4031200-4058400	Weak transcription	Gastric	stomach
27	chr7:4031400-4037000	Weak transcription	Fetal Stomach	stomach
28	chr7:4031400-4037400	Weak transcription	Aorta	Aorta
29	chr7:4031400-4037400	Weak transcription	Spleen	Spleen
30	chr7:4031600-4032000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr7:4031800-4032200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr7:4031800-4037400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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