Variant report

Variant	rs1297990
Chromosome Location	chr1:227060342-227060343
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	chr1:227058010..227060717-chr1:227127922..227130467,2	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10753428	0.97[EUR][1000 genomes]
rs11405	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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150895	0.92[CEU][hapmap]
rs11590925	0.91[CEU][hapmap]
rs12401969	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1295621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1295644	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1295645	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1295646	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1295651	0.92[CEU][hapmap]
rs1295652	0.87[ASW][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1782530	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1794036	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800678	1.00[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs2073488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2105822	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2236910	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236913	1.00[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs2793462	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2802267	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2855563	0.92[CEU][hapmap]
rs6426545	0.92[CEU][hapmap]
rs743601	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7525811	0.92[CEU][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	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1297990	LEFTY1	cis	cerebellum	SCAN
rs1297990	GJC2	cis	parietal	SCAN
rs1297990	PYCR2	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227057800-227060600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227059000-227060400	Flanking Active TSS	HSMMtube	muscle
3	chr1:227059000-227061800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:227059000-227066800	Weak transcription	Aorta	Aorta
5	chr1:227059200-227060600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:227059200-227060600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:227059200-227060600	Enhancers	Placenta	Placenta
8	chr1:227059200-227060600	Enhancers	Left Ventricle	heart
9	chr1:227059200-227060600	Enhancers	Lung	lung
10	chr1:227059200-227060600	Enhancers	HUVEC	blood vessel
11	chr1:227059200-227061000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:227059200-227063600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:227059200-227069000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:227059400-227060400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:227059400-227060400	Enhancers	GM12878-XiMat	blood
16	chr1:227059400-227060400	Enhancers	K562	blood
17	chr1:227059400-227060600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:227059400-227060600	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:227059400-227060600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:227059400-227060600	Enhancers	Fetal Intestine Large	intestine
21	chr1:227059400-227063400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:227059400-227063400	Weak transcription	NH-A	brain
23	chr1:227059400-227069600	Weak transcription	Primary B cells from cord blood	blood
24	chr1:227059600-227060600	Enhancers	Adipose Nuclei	Adipose
25	chr1:227059600-227060600	Enhancers	Liver	Liver
26	chr1:227059600-227060600	Enhancers	Gastric	stomach
27	chr1:227059600-227060600	Enhancers	Stomach Mucosa	stomach
28	chr1:227059600-227063200	Weak transcription	NHEK	skin
29	chr1:227059600-227066000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:227059600-227068400	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:227059600-227069200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:227059600-227070200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:227059800-227060400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr1:227059800-227060400	Enhancers	Colon Smooth Muscle	Colon
35	chr1:227059800-227060600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr1:227059800-227060600	Enhancers	NHLF	lung
37	chr1:227059800-227061400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:227059800-227061600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:227059800-227061600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:227059800-227062200	Weak transcription	A549	lung
41	chr1:227059800-227062600	Weak transcription	Fetal Intestine Small	intestine
42	chr1:227059800-227062600	Weak transcription	Right Ventricle	heart
43	chr1:227059800-227063400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:227059800-227063400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:227059800-227063400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:227059800-227063600	Weak transcription	Colonic Mucosa	Colon
47	chr1:227059800-227064400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:227059800-227064400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:227059800-227064600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr1:227059800-227064600	Weak transcription	Rectal Mucosa Donor 29	rectum

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