Variant report

Variant	rs12143853
Chromosome Location	chr1:212483967-212483968
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	SPI1	chr1:212483759-212484132	GM12878	blood:	n/a	n/a
2	SPI1	chr1:212483740-212484204	HL-60	blood:	n/a	n/a
3	SPI1	chr1:212483784-212484098	GM12891	blood:	n/a	n/a
4	SPI1	chr1:212483727-212484105	HL-60	blood:	n/a	n/a
5	TCF7L2	chr1:212483937-212484403	PANC-1	pancreas:	n/a	n/a
6	SPI1	chr1:212483845-212483984	GM12878	blood:	n/a	n/a
7	SPI1	chr1:212483744-212484071	GM12891	blood:	n/a	n/a
8	SPI1	chr1:212483842-212484019	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212456717..212458394-chr1:212483325..212485097,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225338	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1056985	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863955	1.00[CEU][hapmap]
rs10863956	1.00[AFR][1000 genomes]
rs10863965	1.00[CEU][hapmap]
rs11119886	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs11119891	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs11119893	1.00[AFR][1000 genomes]
rs11119903	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11119907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119910	0.89[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119918	0.91[ASN][1000 genomes]
rs11119927	0.80[EUR][1000 genomes]
rs11119932	1.00[CEU][hapmap]
rs11119934	0.91[CEU][hapmap]
rs12118709	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12118732	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12119779	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12124582	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12128123	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12128965	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12129267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12133582	1.00[CEU][hapmap]
rs12133636	0.89[ASN][1000 genomes]
rs12134074	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12134599	0.87[ASN][1000 genomes]
rs12136095	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12137798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138533	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140158	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12141427	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12145170	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12145377	0.89[CEU][hapmap]
rs12145484	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12146141	1.00[AFR][1000 genomes]
rs12403586	1.00[CEU][hapmap]
rs12561785	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12562618	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1342152	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs14123	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1493601	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17018777	1.00[CEU][hapmap]
rs17018847	1.00[CEU][hapmap]
rs17018853	1.00[CEU][hapmap]
rs1826214	0.81[CEU][hapmap]
rs2236598	0.90[ASN][1000 genomes]
rs2298115	0.82[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3820513	1.00[CEU][hapmap]
rs4951597	1.00[CEU][hapmap]
rs903119	1.00[CEU][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1806604	chr1:212468974-212505860	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12143853	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs12143853	PPP2R5A	cis	Whole Blood	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
2	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
3	chr1:212466200-212506400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:212466600-212503000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:212467400-212526000	Weak transcription	A549	lung
6	chr1:212474200-212484000	Weak transcription	Primary B cells from cord blood	blood
7	chr1:212474200-212502800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:212474600-212489200	Weak transcription	Gastric	stomach
9	chr1:212475200-212487000	Weak transcription	HSMMtube	muscle
10	chr1:212475400-212487000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:212475600-212488600	Weak transcription	Fetal Heart	heart
12	chr1:212477000-212484000	Weak transcription	Osteobl	bone
13	chr1:212478200-212495800	Weak transcription	Fetal Thymus	thymus
14	chr1:212479200-212525400	Weak transcription	Aorta	Aorta
15	chr1:212479600-212489000	Weak transcription	Small Intestine	intestine
16	chr1:212479600-212489200	Weak transcription	Stomach Mucosa	stomach
17	chr1:212479800-212484600	Weak transcription	NHEK	skin
18	chr1:212480200-212484400	Strong transcription	Fetal Intestine Large	intestine
19	chr1:212480400-212484000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr1:212480400-212484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:212480400-212485400	Weak transcription	HMEC	breast
22	chr1:212480600-212484200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:212480600-212489400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:212480800-212488400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:212481200-212484000	Strong transcription	Fetal Stomach	stomach
26	chr1:212481200-212484200	Weak transcription	Placenta	Placenta
27	chr1:212481200-212484600	Strong transcription	Primary T cells from cord blood	blood
28	chr1:212481400-212484800	Strong transcription	Fetal Intestine Small	intestine
29	chr1:212481600-212485800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:212481600-212488600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:212481800-212484400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:212481800-212484400	Strong transcription	Thymus	Thymus
33	chr1:212482000-212484000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:212482400-212484000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:212482400-212484400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr1:212482400-212484800	Enhancers	Left Ventricle	heart
37	chr1:212482600-212484000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:212482600-212486000	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr1:212482600-212486200	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:212482600-212488800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:212482800-212484000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr1:212482800-212484000	Strong transcription	Fetal Lung	lung
43	chr1:212482800-212484200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr1:212482800-212484200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr1:212482800-212484200	Genic enhancers	HepG2	liver
46	chr1:212482800-212484200	Strong transcription	K562	blood
47	chr1:212482800-212484400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:212482800-212484400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr1:212483000-212484200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr1:212483000-212484400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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