Variant report

Variant	rs34949976
Chromosome Location	chr12:31646642-31646643
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	chr12:31645308..31649621-chr12:31742506..31745309,6	MCF-7	breast:
2	chr12:31645681..31648505-chr12:31649831..31652317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255867	Chromatin interaction
ENSG00000170456	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1038066	0.87[EUR][1000 genomes]
rs1269139	0.80[EUR][1000 genomes]
rs12809140	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12812075	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812141	1.00[ASN][1000 genomes]
rs12816170	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816386	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818749	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12819062	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12820294	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12821808	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822601	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825207	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12826193	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12831480	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17497517	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17497656	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17497998	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1879399	1.00[ASN][1000 genomes]
rs2126897	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34007930	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34094545	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34184789	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34271764	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34308937	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34450466	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585237	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34642866	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34667511	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34955459	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34986122	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35029695	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35193529	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35545963	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35567364	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35679974	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35692484	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35981245	0.81[AMR][1000 genomes]
rs3850967	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4338625	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4930977	0.84[AMR][1000 genomes]
rs4930981	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4930983	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4931485	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931498	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931503	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931504	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931510	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4931518	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55635343	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55643034	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55771933	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56183451	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56234529	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56282720	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56327034	1.00[ASN][1000 genomes]
rs56409505	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66479670	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66520413	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66552209	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66597773	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66635949	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67415228	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67963293	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68030436	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455664	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71455667	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71455668	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455669	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455670	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71455671	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73080503	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73084486	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73086471	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73088505	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73088597	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS 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	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31577800-31649400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:31583400-31662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:31594400-31648400	Weak transcription	Small Intestine	intestine
4	chr12:31605400-31647200	Weak transcription	Psoas Muscle	Psoas
5	chr12:31628800-31655800	Weak transcription	Gastric	stomach
6	chr12:31630400-31655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:31633000-31648800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:31633000-31651600	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:31633000-31652400	Weak transcription	Fetal Brain Female	brain
10	chr12:31633200-31647200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:31633200-31647200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:31633200-31647400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:31633200-31649200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:31633200-31649600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:31633200-31652200	Weak transcription	Adipose Nuclei	Adipose
16	chr12:31636200-31647200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:31636200-31663000	Weak transcription	Aorta	Aorta
18	chr12:31637600-31648800	Weak transcription	Fetal Stomach	stomach
19	chr12:31639000-31655800	Weak transcription	Left Ventricle	heart
20	chr12:31640600-31650400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:31641800-31649000	Strong transcription	Primary B cells from cord blood	blood
22	chr12:31642600-31670000	Weak transcription	Fetal Lung	lung
23	chr12:31642800-31647200	Weak transcription	Ovary	ovary
24	chr12:31643200-31647200	Weak transcription	GM12878-XiMat	blood
25	chr12:31643400-31647600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr12:31643600-31648400	Enhancers	Hela-S3	cervix
27	chr12:31643600-31658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:31644000-31647000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:31644000-31648000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr12:31644000-31648200	Strong transcription	HepG2	liver
31	chr12:31644400-31659400	Weak transcription	Pancreas	Pancrea
32	chr12:31644800-31650000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:31645000-31647800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:31645200-31647200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:31645200-31650200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr12:31645400-31647200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:31645400-31647200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:31645400-31647400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:31645400-31647600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:31645400-31648400	Weak transcription	Stomach Mucosa	stomach
41	chr12:31645400-31648800	Strong transcription	Fetal Intestine Large	intestine
42	chr12:31645400-31650000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:31645600-31647200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:31645600-31647600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:31645600-31658000	Weak transcription	Fetal Intestine Small	intestine
46	chr12:31645800-31646800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:31645800-31647200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:31645800-31649000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:31645800-31649200	Weak transcription	NHDF-Ad	bronchial
50	chr12:31645800-31649400	Weak transcription	NHLF	lung

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