Variant report

Variant	rs270712
Chromosome Location	chr1:45051049-45051050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45050697..45052579-chr1:45054486..45057426,3	K562	blood:
2	chr1:45050682..45053753-chr1:45072593..45074247,3	K562	blood:
3	chr1:45050855..45053060-chr1:45080910..45083172,2	K562	blood:
4	chr1:45043963..45046005-chr1:45050905..45053164,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10890309	0.90[CEU][hapmap];0.84[CHB][hapmap];0.87[EUR][1000 genomes]
rs156651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs156652	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270703	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs270706	0.92[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs270707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270710	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270711	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270713	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs270714	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs270716	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs270719	0.95[ASN][1000 genomes]
rs270760	0.89[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs270761	0.87[EUR][1000 genomes]
rs275075	0.92[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs275079	0.99[ASN][1000 genomes]
rs6429543	0.98[ASN][1000 genomes]
rs69141	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs270712	ZNF642	cis	parietal	SCAN
rs270712	GPBP1L1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45018000-45082600	Weak transcription	Right Atrium	heart
2	chr1:45043200-45051600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:45046600-45054800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:45046800-45053600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:45047800-45060000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:45048200-45053400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:45048600-45052000	Enhancers	Brain Hippocampus Middle	brain
8	chr1:45048800-45053000	Strong transcription	Primary hematopoietic stem cells	blood
9	chr1:45049000-45052600	Enhancers	Brain Substantia Nigra	brain
10	chr1:45049000-45062800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr1:45049600-45051200	Enhancers	Fetal Intestine Small	intestine
12	chr1:45049600-45051600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr1:45049800-45051400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:45050000-45053400	Weak transcription	Brain Anterior Caudate	brain
15	chr1:45050000-45057600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:45050200-45051200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:45050400-45051200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:45050400-45051400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:45050400-45051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:45050400-45053400	Weak transcription	Hela-S3	cervix
21	chr1:45050600-45051600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
22	chr1:45050600-45051800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:45050600-45051800	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:45050800-45051200	Enhancers	Brain Angular Gyrus	brain
25	chr1:45050800-45051200	Bivalent Enhancer	Colonic Mucosa	Colon
26	chr1:45050800-45051200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
27	chr1:45050800-45051400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:45050800-45051400	Bivalent Enhancer	Fetal Kidney	kidney
29	chr1:45051000-45051200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:45051000-45051200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
31	chr1:45051000-45051200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr1:45051000-45051200	Enhancers	Pancreas	Pancrea
33	chr1:45051000-45051600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
34	chr1:45051000-45052400	Bivalent Enhancer	Fetal Intestine Large	intestine

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