Variant report

Variant	rs7967230
Chromosome Location	chr12:12541869-12541870
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	chr12:12538899..12542001-chr12:12714080..12716309,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1019340	0.84[JPT][hapmap];0.88[MEX][hapmap]
rs1030069	0.83[JPT][hapmap]
rs10459098	0.84[JPT][hapmap]
rs10743982	0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs10845530	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs10845539	0.84[JPT][hapmap];0.88[MEX][hapmap]
rs10845545	0.83[JPT][hapmap]
rs10845546	0.84[JPT][hapmap]
rs11561172	0.89[JPT][hapmap]
rs11609375	0.84[JPT][hapmap];0.88[MEX][hapmap]
rs2193270	0.84[JPT][hapmap]
rs3925170	0.84[JPT][hapmap];0.87[MEX][hapmap]
rs4763825	0.84[JPT][hapmap];0.84[MEX][hapmap]
rs4763829	0.84[JPT][hapmap];0.88[MEX][hapmap]
rs4763830	0.84[JPT][hapmap];0.88[MEX][hapmap]
rs6488520	0.84[JPT][hapmap]
rs7295080	0.84[JPT][hapmap];0.96[MEX][hapmap]
rs73061463	0.84[ASN][1000 genomes]
rs7309503	0.82[ASW][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs7309982	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7310012	0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs7311363	0.85[ASN][1000 genomes]
rs7311364	0.84[JPT][hapmap];0.88[MEX][hapmap]
rs7313825	0.84[JPT][hapmap];0.88[MEX][hapmap]
rs73283441	0.82[ASN][1000 genomes]
rs7953025	0.84[JPT][hapmap];0.96[MEX][hapmap]
rs7967111	0.86[GIH][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap]
rs7967466	0.89[JPT][hapmap]
rs7969849	0.84[JPT][hapmap];0.84[MEX][hapmap]
rs888200	0.84[JPT][hapmap];0.96[MEX][hapmap];0.81[ASN][1000 genomes]
rs9645752	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:41 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1036040	chr12:12506839-12541869	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1037542	chr12:12506839-12542868	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS 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	17 gene(s)	inside rSNPs	diseases
5	nsv1045637	chr12:12506839-12546747	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv1052243	chr12:12512726-12541869	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv1051597	chr12:12513364-12541869	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv557584	chr12:12514203-12541869	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv818893	chr12:12515184-12541869	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv1050133	chr12:12519319-12541869	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv1049869	chr12:12519319-12542868	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1047762	chr12:12520906-12541869	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	esv2760275	chr12:12530073-12546759	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv557585	chr12:12530718-12541869	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv818894	chr12:12530718-12541869	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv437141	chr12:12530718-12544266	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	esv3483107	chr12:12531330-12542599	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	esv3483096	chr12:12531345-12542593	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	esv3483118	chr12:12531345-12542593	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	esv3483085	chr12:12531375-12542582	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	esv2421794	chr12:12532984-12541869	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv469115	chr12:12532984-12541869	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv469117	chr12:12532984-12541869	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	nsv469118	chr12:12532984-12541869	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	nsv557592	chr12:12532984-12541869	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
27	nsv557593	chr12:12532984-12543233	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
28	nsv818895	chr12:12532984-12544266	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
29	nsv517152	chr12:12532984-12547645	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	nsv1041842	chr12:12536207-12546747	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	esv2760855	chr12:12536219-12541869	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	nsv442636	chr12:12537497-12541871	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	nsv557596	chr12:12537608-12541869	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	nsv557597	chr12:12537608-12543233	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
35	nsv557599	chr12:12537838-12543233	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
36	nsv557600	chr12:12538068-12541869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
37	nsv557601	chr12:12538135-12541869	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
38	nsv557603	chr12:12538410-12543233	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
39	nsv557604	chr12:12538775-12541869	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
40	nsv557605	chr12:12540376-12541869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
41	nsv557606	chr12:12540376-12543233	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7967230	ETV6	cis	cerebellum	SCAN
rs7967230	AICDA	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12511600-12550600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:12512000-12545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:12519200-12549800	Weak transcription	Aorta	Aorta
4	chr12:12521800-12542800	Weak transcription	Adipose Nuclei	Adipose
5	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:12525400-12550200	Weak transcription	Fetal Stomach	stomach
7	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:12532800-12556400	Weak transcription	Spleen	Spleen
9	chr12:12533000-12542800	Weak transcription	Placenta	Placenta
10	chr12:12533000-12545800	Weak transcription	Pancreas	Pancrea
11	chr12:12533400-12555800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr12:12533600-12555400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr12:12535400-12542800	Weak transcription	Right Ventricle	heart
14	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:12535800-12542600	Weak transcription	Lung	lung
16	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
17	chr12:12538200-12551000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:12538400-12545800	Weak transcription	Left Ventricle	heart
19	chr12:12538400-12548600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:12538400-12549200	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:12538400-12550200	Weak transcription	Primary T cells from cord blood	blood
22	chr12:12538400-12551600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:12538400-12552800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:12538400-12555400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:12538400-12556200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:12538800-12551400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:12539400-12542000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:12539400-12546800	Weak transcription	Stomach Mucosa	stomach
30	chr12:12539600-12545200	Weak transcription	Fetal Intestine Small	intestine
31	chr12:12539800-12545800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr12:12540200-12545000	Weak transcription	HepG2	liver
33	chr12:12540200-12545200	Weak transcription	Fetal Intestine Large	intestine
34	chr12:12540200-12560600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:12540400-12542000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:12540400-12542000	Enhancers	Brain Hippocampus Middle	brain
37	chr12:12540600-12549400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:12540600-12556200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr12:12540800-12543600	Weak transcription	Thymus	Thymus
40	chr12:12540800-12543800	Weak transcription	Fetal Thymus	thymus
41	chr12:12540800-12550800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:12540800-12551000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:12540800-12553800	Weak transcription	GM12878-XiMat	blood
44	chr12:12540800-12555400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr12:12541000-12542000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:12541000-12543600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:12541000-12543800	Weak transcription	K562	blood
48	chr12:12541000-12545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:12541000-12545000	Weak transcription	Fetal Lung	lung
50	chr12:12541000-12545200	Weak transcription	Fetal Heart	heart

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