Variant report

Variant	rs7548543
Chromosome Location	chr1:150203652-150203653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150189218..150190851-chr1:150202612..150205022,2	K562	blood:
2	chr1:150203436..150211066-chr1:150333611..150339492,20	K562	blood:
3	chr1:150187895..150191016-chr1:150200344..150204112,3	K562	blood:
4	chr1:150198495..150205043-chr1:150206226..150211170,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143401	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000222222	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10788872	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10888575	0.94[ASN][1000 genomes]
rs10888576	0.99[ASN][1000 genomes]
rs11205339	0.94[ASN][1000 genomes]
rs11205340	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11205341	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs11205343	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11205347	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs11205348	0.94[ASN][1000 genomes]
rs11811787	0.99[ASN][1000 genomes]
rs12057558	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs12131063	0.94[ASN][1000 genomes]
rs12133235	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12133238	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12569047	0.93[ASN][1000 genomes]
rs1535873	0.94[ASN][1000 genomes]
rs1924549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2038752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2038753	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298161	0.92[CEU][hapmap]
rs3118124	0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3121000	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3121001	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35938158	0.88[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs4408187	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55647200	0.99[ASN][1000 genomes]
rs55956539	0.99[ASN][1000 genomes]
rs59507173	0.94[ASN][1000 genomes]
rs61161619	0.95[ASN][1000 genomes]
rs6587753	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6655935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6660127	0.94[ASN][1000 genomes]
rs6665499	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680040	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6682434	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692738	0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6694215	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703332	0.92[ASN][1000 genomes]
rs7522034	0.89[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7532164	0.94[ASN][1000 genomes]
rs7535712	0.91[JPT][hapmap]
rs7551023	0.94[ASN][1000 genomes]
rs7555995	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7548543	TNFAIP8L2	cis	cerebellum	SCAN
rs7548543	MRPS21	cis	parietal	SCAN
rs7548543	MRPS21	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150184200-150206600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:150186200-150206800	Weak transcription	Spleen	Spleen
3	chr1:150186400-150206000	Weak transcription	Colonic Mucosa	Colon
4	chr1:150186400-150206800	Weak transcription	Esophagus	oesophagus
5	chr1:150186600-150205200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:150186600-150205800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:150186600-150205800	Weak transcription	Right Atrium	heart
8	chr1:150186600-150206000	Weak transcription	Fetal Brain Male	brain
9	chr1:150186600-150206200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:150186600-150206200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:150186600-150206400	Weak transcription	Aorta	Aorta
12	chr1:150186800-150205800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:150186800-150205800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:150186800-150205800	Weak transcription	Brain Germinal Matrix	brain
15	chr1:150186800-150205800	Weak transcription	Brain Substantia Nigra	brain
16	chr1:150186800-150206800	Weak transcription	Pancreas	Pancrea
17	chr1:150189000-150204600	Strong transcription	Dnd41	blood
18	chr1:150190800-150204400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:150190800-150204400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:150190800-150204400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:150191200-150204400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:150191200-150204400	Strong transcription	Fetal Thymus	thymus
23	chr1:150191400-150204400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:150191600-150204200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:150191600-150205400	Weak transcription	Small Intestine	intestine
26	chr1:150191800-150204200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:150191800-150205000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:150192000-150204200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:150192000-150204400	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:150192200-150203800	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr1:150192800-150203800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:150192800-150206800	Weak transcription	Gastric	stomach
33	chr1:150193000-150204200	Strong transcription	Fetal Stomach	stomach
34	chr1:150193400-150204000	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:150194000-150203800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:150194200-150203800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:150194400-150205000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:150195000-150203800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:150195200-150203800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:150195200-150204400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:150195400-150203800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:150195400-150204400	Strong transcription	Osteobl	bone
43	chr1:150195600-150204400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:150196800-150204000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:150196800-150204400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:150197000-150204200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:150197600-150205200	Weak transcription	Fetal Heart	heart
48	chr1:150197800-150205800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:150198200-150206600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:150198600-150205400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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