Variant report

Variant	rs3770770
Chromosome Location	chr2:37192866-37192867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37191677..37193362-chr2:37233119..37235779,2	K562	blood:
2	chr2:37186145..37190956-chr2:37191183..37194668,5	K562	blood:
3	chr2:37114816..37116390-chr2:37191550..37193356,2	MCF-7	breast:
4	chr2:37183661..37187179-chr2:37192061..37194972,3	MCF-7	breast:
5	chr2:37192443..37195662-chr2:37309226..37313144,4	K562	blood:
6	chr2:37170595..37172882-chr2:37190992..37193264,2	K562	blood:

Variant related genes	Relation type
ENSG00000252518	Chromatin interaction
ENSG00000152133	Chromatin interaction
ENSG00000008869	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1007823	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs10084334	0.81[JPT][hapmap]
rs10167385	0.81[JPT][hapmap]
rs10490658	0.91[CHB][hapmap]
rs10495869	0.95[JPT][hapmap];0.88[MEX][hapmap]
rs1123648	0.83[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11682782	0.81[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes]
rs11685402	0.95[JPT][hapmap]
rs11688446	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11694342	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17020071	0.86[CHB][hapmap]
rs17020125	0.83[CEU][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs17020136	0.89[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17020143	0.95[JPT][hapmap]
rs17038861	0.83[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17443495	0.81[CHB][hapmap]
rs2160411	0.85[JPT][hapmap]
rs2372788	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3796041	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4670642	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4670645	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59952755	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60572996	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61380056	0.80[AMR][1000 genomes]
rs61689754	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62133071	0.80[AMR][1000 genomes]
rs62133077	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62133080	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62133081	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62133082	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62133104	0.86[EUR][1000 genomes]
rs62133105	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62133107	0.85[EUR][1000 genomes]
rs62133108	0.87[EUR][1000 genomes]
rs6709006	0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs6712162	0.80[AMR][1000 genomes]
rs6723869	0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6728062	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6753260	0.83[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9636389	0.83[ASN][1000 genomes]
rs9636428	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9636429	0.80[AMR][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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv456363	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv581470	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3440334	chr2:37192273-37194821	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv3344704	chr2:37192448-37195146	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3770770	STRN	cis	multi-tissue	Pritchard
rs3770770	STRN	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37191600-37193200	Flanking Active TSS	Dnd41	blood
2	chr2:37191600-37194600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:37191600-37194600	Active TSS	NHLF	lung
4	chr2:37191800-37193000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr2:37191800-37193000	Active TSS	Right Atrium	heart
6	chr2:37191800-37193200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:37191800-37193200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:37191800-37193200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr2:37191800-37194000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:37191800-37194400	Active TSS	Esophagus	oesophagus
11	chr2:37191800-37194600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr2:37191800-37194600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:37191800-37194600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:37191800-37194600	Active TSS	Left Ventricle	heart
15	chr2:37191800-37195000	Active TSS	NHDF-Ad	bronchial
16	chr2:37192000-37193000	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr2:37192000-37193000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr2:37192000-37193000	Flanking Active TSS	Fetal Lung	lung
19	chr2:37192000-37193200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr2:37192000-37193200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:37192000-37193200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr2:37192000-37194000	Active TSS	Colonic Mucosa	Colon
23	chr2:37192000-37194200	Active TSS	HSMM	muscle
24	chr2:37192000-37194400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr2:37192000-37194400	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr2:37192000-37194400	Active TSS	NH-A	brain
27	chr2:37192000-37194800	Active TSS	Right Ventricle	heart
28	chr2:37192000-37195000	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr2:37192000-37195000	Active TSS	Psoas Muscle	Psoas
30	chr2:37192200-37193000	Flanking Active TSS	Fetal Brain Female	brain
31	chr2:37192200-37193200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr2:37192200-37193200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:37192200-37193200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr2:37192200-37194400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:37192200-37194400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:37192200-37194400	Active TSS	Fetal Brain Male	brain
37	chr2:37192200-37194600	Active TSS	Duodenum Mucosa	Duodenum
38	chr2:37192200-37194600	Active TSS	Ovary	ovary
39	chr2:37192200-37194600	Active TSS	GM12878-XiMat	blood
40	chr2:37192200-37194800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr2:37192200-37194800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr2:37192200-37194800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:37192200-37194800	Active TSS	Rectal Smooth Muscle	rectum
44	chr2:37192200-37195000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:37192200-37195000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:37192400-37193000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr2:37192400-37193000	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr2:37192400-37194000	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr2:37192400-37194200	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr2:37192400-37194200	Active TSS	iPS-18 Cell Line	embryonic stem cell

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