Variant report

Variant	rs10846411
Chromosome Location	chr12:8206167-8206168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:8184759..8186737-chr12:8205565..8207899,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065970	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11057065	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12321718	0.86[GIH][hapmap]
rs2072448	0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2072449	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2110070	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782680	0.86[GIH][hapmap]
rs3782683	0.80[CHB][hapmap];0.86[GIH][hapmap]
rs4883479	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4883480	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048545	chr12:7778760-8608231	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv541368	chr12:7778760-8608231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	esv1795892	chr12:7856819-8508693	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised 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 target site	93 gene(s)	inside rSNPs	diseases
6	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
7	esv1797934	chr12:7985460-8214261	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	esv1793572	chr12:7995827-8568422	Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv1040972	chr12:8003413-8266291	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
10	nsv541388	chr12:8003413-8266291	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
11	nsv916941	chr12:8003501-8608220	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic 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	86 gene(s)	inside rSNPs	diseases
12	nsv1045521	chr12:8123225-8242846	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
13	nsv1040958	chr12:8177050-8309724	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv541396	chr12:8177050-8309724	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10846411	C3AR1	cis	lung	GTEx
rs10846411	DYRK4	cis	cerebellum	SCAN
rs10846411	NECAP1	cis	Whole Blood	GTEx
rs10846411	FOXJ2	cis	Whole Blood	GTEx
rs10846411	C3AR1	cis	Whole Blood	GTEx
rs10846411	ANO2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8191800-8208400	Strong transcription	Dnd41	blood
2	chr12:8192000-8208000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:8192000-8208200	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr12:8192000-8208600	Strong transcription	Fetal Stomach	stomach
5	chr12:8192000-8211000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:8192200-8207600	Strong transcription	Placenta	Placenta
7	chr12:8192200-8207800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr12:8192200-8208000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:8192200-8208000	Strong transcription	Fetal Lung	lung
10	chr12:8192200-8208200	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:8192200-8208200	Strong transcription	Fetal Intestine Large	intestine
12	chr12:8192200-8208400	Strong transcription	Liver	Liver
13	chr12:8192200-8208600	Strong transcription	Primary T cells from cord blood	blood
14	chr12:8192400-8206200	Strong transcription	Brain Angular Gyrus	brain
15	chr12:8192400-8206800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:8192400-8207600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:8192400-8208000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:8192400-8208000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:8192400-8208000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:8192400-8208200	Strong transcription	Fetal Thymus	thymus
21	chr12:8192400-8208400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:8192400-8208400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:8192400-8208400	Strong transcription	Brain Hippocampus Middle	brain
24	chr12:8192400-8208400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr12:8192400-8208400	Strong transcription	Osteobl	bone
26	chr12:8192400-8208600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:8192400-8209200	Strong transcription	Adipose Nuclei	Adipose
28	chr12:8192400-8211000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:8192600-8208200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:8192600-8208400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:8192600-8208400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:8192600-8208400	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:8192600-8208400	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:8192600-8208600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr12:8192600-8212400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:8192800-8208400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:8192800-8208400	Strong transcription	Left Ventricle	heart
38	chr12:8192800-8208400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:8193200-8208400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:8193400-8208400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:8198400-8208400	Strong transcription	A549	lung
42	chr12:8198800-8208400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:8199000-8208000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:8199000-8208000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:8199000-8208000	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr12:8199000-8208200	Strong transcription	Brain Cingulate Gyrus	brain
47	chr12:8199000-8208400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:8199000-8208400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:8199000-8208400	Strong transcription	Colon Smooth Muscle	Colon
50	chr12:8199200-8208200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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