Variant report

Variant	rs3790606
Chromosome Location	chr1:113052186-113052187
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113051455..113054966-chr1:113056475..113060104,3	MCF-7	breast:
2	chr1:113050916..113052536-chr1:113056260..113057826,2	K562	blood:
3	chr1:113050070..113052532-chr1:113159337..113161675,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000007341	Chromatin interaction
ENSG00000134245	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11102484	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102514	0.82[CHB][hapmap]
rs12049572	0.86[CHB][hapmap]
rs12120956	0.85[CHB][hapmap]
rs12122980	0.82[CHB][hapmap]
rs12130243	0.82[CHB][hapmap]
rs12136566	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12756815	0.84[CHB][hapmap]
rs17030613	0.82[CHB][hapmap]
rs2273368	0.91[CHB][hapmap]
rs3737136	0.91[CHB][hapmap]
rs3790605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828074	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1008375	chr1:113028271-113060221	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1009068	chr1:113048992-113057407	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3790606	ST7L	cis	parietal	SCAN
rs3790606	WNT2B	cis	parietal	SCAN
rs3790606	ST7L	cis	lymphoblastoid	seeQTL
rs3790606	DENND2C	cis	parietal	SCAN
rs3790606	SLC16A4	cis	cerebellum	SCAN
rs3790606	ST7L	cis	multi-tissue	Pritchard

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113050000-113052400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:113050200-113052200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
3	chr1:113050200-113052200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:113050200-113052200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:113050200-113052200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
6	chr1:113050200-113052400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:113050200-113052400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:113050200-113052400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:113050200-113052800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:113050400-113052200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
11	chr1:113050400-113052200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:113050400-113052200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:113050400-113052200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:113050400-113052200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:113050400-113052200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
16	chr1:113050400-113052400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:113050400-113052400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:113050400-113052800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr1:113050600-113052200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:113050600-113052200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:113050600-113052200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:113050600-113052200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:113050600-113052400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:113050800-113052200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:113050800-113052200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
26	chr1:113051000-113052200	Transcr. at gene 5' and 3'	Right Atrium	heart
27	chr1:113051200-113052600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:113051200-113052600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:113051200-113053200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:113051400-113052200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:113051400-113052200	Bivalent Enhancer	Liver	Liver
32	chr1:113051400-113052200	Active TSS	Brain Anterior Caudate	brain
33	chr1:113051400-113052200	Active TSS	Brain Substantia Nigra	brain
34	chr1:113051400-113052200	Bivalent/Poised TSS	Fetal Brain Female	brain
35	chr1:113051400-113052200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
36	chr1:113051400-113052400	Active TSS	Hela-S3	cervix
37	chr1:113051400-113052600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:113051400-113052600	Active TSS	Lung	lung
39	chr1:113051400-113053000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
40	chr1:113051400-113053200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
41	chr1:113051400-113053600	Bivalent/Poised TSS	Fetal Stomach	stomach
42	chr1:113051600-113052200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
43	chr1:113051600-113052200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
44	chr1:113051600-113052200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr1:113051600-113052200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr1:113051600-113052200	Bivalent/Poised TSS	Osteobl	bone
47	chr1:113051600-113052400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
48	chr1:113051800-113052200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:113051800-113052200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:113051800-113052200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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