Variant report

Variant	rs6766451
Chromosome Location	chr3:196375140-196375141
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196372018..196375838-chr3:196376794..196379332,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11709911	1.00[ASN][1000 genomes]
rs11710998	1.00[ASN][1000 genomes]
rs11720010	1.00[ASN][1000 genomes]
rs11918382	0.97[ASN][1000 genomes]
rs34282171	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv1003135	chr3:196348721-196738953	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
10	nsv1013920	chr3:196370580-196452741	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1014526	chr3:196372422-196460169	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008083	chr3:196374919-196460768	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv536897	chr3:196374919-196460768	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6766451	IQCG	cis	cerebellum	SCAN
rs6766451	PIGX	cis	cerebellum	SCAN
rs6766451	UBXN7	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196367200-196393200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:196367600-196376800	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:196367600-196386800	Weak transcription	Gastric	stomach
4	chr3:196367600-196393200	Weak transcription	Brain Substantia Nigra	brain
5	chr3:196367800-196392800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:196367800-196393000	Weak transcription	Brain Anterior Caudate	brain
7	chr3:196367800-196397000	Weak transcription	Fetal Intestine Small	intestine
8	chr3:196368000-196377800	Weak transcription	Esophagus	oesophagus
9	chr3:196368800-196377400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:196369000-196377600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:196369600-196375600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:196369600-196377800	Weak transcription	Left Ventricle	heart
13	chr3:196369600-196388800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:196370000-196377200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:196370200-196381400	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr3:196370200-196381800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:196370200-196381800	Genic enhancers	Fetal Thymus	thymus
18	chr3:196370600-196381200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:196370800-196375800	Weak transcription	Thymus	Thymus
20	chr3:196371000-196376200	Genic enhancers	GM12878-XiMat	blood
21	chr3:196371200-196376200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr3:196371200-196377600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:196371200-196377800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:196371200-196383200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:196371400-196390000	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:196371800-196377400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:196372000-196378800	Weak transcription	Right Ventricle	heart
28	chr3:196372200-196376200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:196372400-196375800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:196372400-196378800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:196372800-196376200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:196372800-196377400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:196372800-196378000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:196373000-196375800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:196373000-196376400	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr3:196373000-196381000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:196373000-196392000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:196373200-196376800	Genic enhancers	Monocytes-CD14+_RO01746	blood
39	chr3:196373200-196377400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:196373200-196377600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:196373400-196380200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:196373600-196375800	Weak transcription	Primary B cells from cord blood	blood
43	chr3:196373600-196375800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:196373600-196377600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:196373600-196377600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:196373600-196378200	Weak transcription	Lung	lung
47	chr3:196373600-196383200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:196373600-196392000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:196373800-196375600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr3:196373800-196375800	Weak transcription	H9 Cell Line	embryonic stem cell

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