Variant report

Variant	rs7954
Chromosome Location	chr22:30184950-30184951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30183374..30186087-chr22:30189628..30192258,4	MCF-7	breast:
2	chr22:30127476..30130014-chr22:30183535..30186061,2	MCF-7	breast:
3	chr22:30182549..30186689-chr22:30188373..30192437,4	K562	blood:
4	chr22:30181656..30186213-chr22:30190409..30196916,8	MCF-7	breast:
5	chr22:30183311..30186550-chr22:30186984..30189560,4	MCF-7	breast:
6	chr22:30182549..30185414-chr22:30188242..30189873,2	K562	blood:
7	chr22:30182004..30185271-chr22:30192660..30196046,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs131267	0.84[EUR][1000 genomes]
rs131268	0.83[EUR][1000 genomes]
rs131284	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs131287	0.86[EUR][1000 genomes]
rs131298	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131301	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs140114	0.81[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs140117	0.84[EUR][1000 genomes]
rs140119	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs140122	0.83[EUR][1000 genomes]
rs140126	0.81[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs140127	0.84[EUR][1000 genomes]
rs140128	0.86[EUR][1000 genomes]
rs140134	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs140139	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs140140	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1961926	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs249396	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249397	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs249398	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs249401	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36576	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs5752961	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs5752962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997534	0.93[ASN][1000 genomes]
rs6006267	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs737945	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs81800	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs9608816	0.87[ASN][1000 genomes]
rs9614055	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription 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 miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS 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 miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active 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 target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7954	CABP7	cis	cerebellum	SCAN
rs7954	INPP5J	cis	cerebellum	SCAN
rs7954	NIPSNAP1	cis	cerebellum	SCAN
rs7954	TTC28	cis	cerebellum	SCAN
rs7954	KIAA1671	cis	cerebellum	SCAN
rs7954	NIPSNAP1	cis	parietal	SCAN
rs7954	MTMR3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30164600-30185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:30164600-30188600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr22:30166800-30194400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr22:30167200-30187800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr22:30167400-30185400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr22:30175400-30194000	Weak transcription	Hela-S3	cervix
7	chr22:30177000-30189000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:30177200-30186000	Weak transcription	Fetal Kidney	kidney
9	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr22:30178400-30193000	Weak transcription	A549	lung
11	chr22:30178800-30186000	Weak transcription	K562	blood
12	chr22:30178800-30186000	Weak transcription	NH-A	brain
13	chr22:30179200-30185600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr22:30180200-30186800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr22:30180800-30187800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr22:30181200-30185400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:30181200-30188200	Weak transcription	Fetal Brain Male	brain
18	chr22:30181200-30196200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr22:30181200-30196200	Weak transcription	Fetal Heart	heart
20	chr22:30181400-30185400	Weak transcription	NHDF-Ad	bronchial
21	chr22:30181400-30185600	Weak transcription	Psoas Muscle	Psoas
22	chr22:30182000-30194600	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr22:30182200-30194000	Strong transcription	Fetal Muscle Leg	muscle
24	chr22:30182200-30217000	Strong transcription	Fetal Intestine Small	intestine
25	chr22:30182200-30222200	Strong transcription	Thymus	Thymus
26	chr22:30182400-30185200	Weak transcription	Fetal Lung	lung
27	chr22:30182400-30192800	Strong transcription	Brain Hippocampus Middle	brain
28	chr22:30182600-30194800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr22:30182800-30185800	Genic enhancers	Spleen	Spleen
30	chr22:30182800-30192000	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr22:30182800-30192800	Strong transcription	Fetal Thymus	thymus
32	chr22:30182800-30194400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr22:30182800-30194600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr22:30182800-30194600	Strong transcription	Stomach Smooth Muscle	stomach
35	chr22:30182800-30204600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr22:30182800-30204800	Strong transcription	Fetal Brain Female	brain
37	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
38	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
39	chr22:30183000-30188600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr22:30183000-30189000	Strong transcription	HUVEC	blood vessel
41	chr22:30183000-30189800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr22:30183000-30191600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr22:30183000-30192600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr22:30183000-30192600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr22:30183000-30192800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr22:30183000-30193000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr22:30183000-30193000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr22:30183000-30193400	Strong transcription	Osteobl	bone
49	chr22:30183000-30194000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr22:30183000-30194200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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