Variant report

Variant	rs781770
Chromosome Location	chr1:44974119-44974120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:44965854..44968248-chr1:44973969..44975941,2	K562	blood:
2	chr1:44965779..44967986-chr1:44972874..44975622,2	K562	blood:
3	chr1:44974069..44975867-chr1:45042813..45044583,2	K562	blood:
4	chr1:44971909..44974855-chr1:44979477..44982336,4	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12562325	0.85[ASN][1000 genomes]
rs270721	0.90[ASN][1000 genomes]
rs272534	0.80[ASN][1000 genomes]
rs2994537	0.94[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs67874053	0.90[ASN][1000 genomes]
rs781772	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs781775	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs781790	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs811928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1010785	chr1:44407804-44974324	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv534938	chr1:44407804-44974324	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	esv1005212	chr1:44972573-44985674	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs781770	RIMS3	cis	parietal	SCAN
rs781770	RAD54L	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:44966200-44975400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:44967600-44975200	Weak transcription	Right Atrium	heart
3	chr1:44968000-44974800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:44970600-44974200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
5	chr1:44970800-44974400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
6	chr1:44970800-44974400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:44971000-44974200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
8	chr1:44971000-44974400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:44971200-44975200	Enhancers	Brain Hippocampus Middle	brain
10	chr1:44971400-44974800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr1:44971600-44975600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:44972400-44974400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr1:44972800-44974400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
14	chr1:44972800-44974800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:44973000-44974200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:44973000-44974800	Enhancers	Brain Anterior Caudate	brain
17	chr1:44973200-44977400	Enhancers	Brain Cingulate Gyrus	brain
18	chr1:44973400-44974200	Enhancers	Brain Germinal Matrix	brain
19	chr1:44973400-44974400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:44973400-44974600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:44973400-44974800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:44973600-44974600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:44973600-44974800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
24	chr1:44973800-44974200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
25	chr1:44973800-44974600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr1:44973800-44974800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
27	chr1:44973800-44983000	Enhancers	Brain Substantia Nigra	brain
28	chr1:44974000-44974200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr1:44974000-44974200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:44974000-44974200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
31	chr1:44974000-44974400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
32	chr1:44974000-44974600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:44974000-44974600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:44974000-44974800	Enhancers	Brain Angular Gyrus	brain
35	chr1:44974000-44975000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:44974000-44975200	Enhancers	Brain Inferior Temporal Lobe	brain

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