Variant report

Variant	rs7522034
Chromosome Location	chr1:150199123-150199124
allele	G/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	SPI1	chr1:150198913-150199137	GM12878	blood:	n/a	n/a
2	SPI1	chr1:150198846-150199152	GM12891	blood:	n/a	n/a
3	SPI1	chr1:150198871-150199180	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150198495..150205043-chr1:150206226..150211170,11	MCF-7	breast:

Variant related genes	Relation type
ANP32E	TF binding region
ENSG00000143401	Chromatin interaction
ENSG00000222222	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10788872	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11205340	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11205341	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11205343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11205347	0.80[GIH][hapmap];0.82[JPT][hapmap]
rs12057558	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs12133235	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12133238	0.95[JPT][hapmap]
rs1924549	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2038752	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2038753	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2298161	0.92[CEU][hapmap]
rs3118124	0.85[GIH][hapmap];0.91[JPT][hapmap]
rs3121000	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3121001	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35938158	0.88[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4408187	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587753	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6655935	0.89[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.82[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]
rs6665499	0.82[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6680040	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6682434	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6692738	0.82[GIH][hapmap];0.91[JPT][hapmap]
rs6694215	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7535712	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7548543	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]
rs7555995	0.82[JPT][hapmap]

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
rs7522034	MRPS21	cis	cerebellum	SCAN
rs7522034	MRPS21	cis	parietal	SCAN
rs7522034	TNFAIP8L2	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	chr1:150190000-150201200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:150190800-150204400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:150190800-150204400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:150190800-150204400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:150191200-150201600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:150191200-150204400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:150191200-150204400	Strong transcription	Fetal Thymus	thymus
25	chr1:150191400-150204400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:150191600-150204200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:150191600-150205400	Weak transcription	Small Intestine	intestine
28	chr1:150191800-150200000	Strong transcription	Fetal Intestine Large	intestine
29	chr1:150191800-150200200	Strong transcription	Hela-S3	cervix
30	chr1:150191800-150200800	Strong transcription	Liver	Liver
31	chr1:150191800-150203200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:150191800-150204200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:150191800-150205000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:150192000-150204200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:150192000-150204400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:150192200-150203800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:150192800-150203800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:150192800-150206800	Weak transcription	Gastric	stomach
39	chr1:150193000-150202000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:150193000-150204200	Strong transcription	Fetal Stomach	stomach
41	chr1:150193400-150204000	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:150194000-150201000	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:150194000-150203800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:150194200-150203800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:150194400-150201600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:150194400-150205000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:150194800-150200400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:150195000-150203800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:150195200-150199600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:150195200-150200200	Strong transcription	HSMM	muscle

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