Variant report

Variant	rs1511049
Chromosome Location	chr1:214786437-214786438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:214773497..214776791-chr1:214785798..214789572,5	K562	blood:
2	chr1:214781048..214782795-chr1:214784568..214786728,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN14-6	chr1:214786303-214786741	NONHSAT009468

Variant related genes	Relation type
ENSG00000250536	Chromatin interaction
ENSG00000117724	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11120364	0.82[CEU][hapmap]
rs11801893	0.94[AMR][1000 genomes]
rs12097854	0.84[CHD][hapmap]
rs12404854	0.82[ASN][1000 genomes]
rs12405890	0.82[ASN][1000 genomes]
rs12405995	0.82[ASN][1000 genomes]
rs12410075	0.82[ASN][1000 genomes]
rs1511050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023274	0.82[ASN][1000 genomes]
rs17023275	0.82[ASN][1000 genomes]
rs17023338	0.84[CHD][hapmap]
rs2070065	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2666834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666839	0.85[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2807662	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2807663	1.00[YRI][hapmap]
rs2809588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748691	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748693	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3795514	0.84[CHD][hapmap]
rs3795516	0.84[CHD][hapmap]
rs41303281	0.82[ASN][1000 genomes]
rs60944459	0.82[ASN][1000 genomes]
rs7522082	0.82[CEU][hapmap]
rs998452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004475	chr1:214763778-215013375	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1005669	chr1:214774522-214994142	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv997864	chr1:214778658-214994142	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1511049	ATF3	cis	parietal	SCAN
rs1511049	SYT14	cis	cerebellum	SCAN
rs1511049	TRAF3IP3	cis	cerebellum	SCAN
rs1511049	DTL	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214777600-214800400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:214777600-214810800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:214777600-214838600	Weak transcription	Esophagus	oesophagus
4	chr1:214777800-214838400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:214778000-214839200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:214778200-214786600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:214778200-214786600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:214778200-214791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:214778200-214791200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:214778200-214793000	Weak transcription	HSMM	muscle
11	chr1:214778200-214793600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:214778200-214793800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:214778200-214803600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:214778400-214786600	Weak transcription	Osteobl	bone
15	chr1:214778400-214786800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:214778400-214794200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:214778600-214788000	Weak transcription	Hela-S3	cervix
18	chr1:214778600-214791200	Weak transcription	NHEK	skin
19	chr1:214778800-214786600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:214778800-214787600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:214778800-214787800	Weak transcription	HepG2	liver
22	chr1:214778800-214788800	Weak transcription	HMEC	breast
23	chr1:214778800-214794000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:214781200-214818000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:214781400-214786800	Weak transcription	NHLF	lung
26	chr1:214781400-214790600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:214781600-214791400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:214781800-214792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:214781800-214794000	Weak transcription	Fetal Stomach	stomach
30	chr1:214781800-214795800	Weak transcription	Fetal Intestine Small	intestine
31	chr1:214782000-214803800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:214782800-214792800	Weak transcription	Thymus	Thymus
33	chr1:214782800-214794000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:214783000-214788600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:214783000-214788800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:214783200-214786600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:214783200-214786600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:214783200-214788000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:214783200-214788400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:214783200-214788800	Weak transcription	GM12878-XiMat	blood
41	chr1:214783200-214790600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:214783200-214790600	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:214783200-214794000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:214783200-214817800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:214783400-214786600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:214783400-214786600	Weak transcription	A549	lung
47	chr1:214783400-214786800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:214783400-214787400	Weak transcription	HUVEC	blood vessel
49	chr1:214783400-214787600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:214783400-214787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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