Variant report

Variant	rs2604052
Chromosome Location	chr12:31728999-31729000
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31727967..31729813-chr12:31742759..31744417,2	K562	blood:
2	chr12:31727734..31729670-chr12:31731593..31733122,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170456	Chromatin interaction
ENSG00000255867	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11051456	0.87[ASN][1000 genomes]
rs1150942	0.91[ASN][1000 genomes]
rs1150943	0.91[ASN][1000 genomes]
rs1150945	0.91[ASN][1000 genomes]
rs1150954	0.91[ASN][1000 genomes]
rs1150955	0.91[ASN][1000 genomes]
rs1150963	0.91[ASN][1000 genomes]
rs1259233	0.91[ASN][1000 genomes]
rs1259241	0.91[ASN][1000 genomes]
rs1259353	0.91[ASN][1000 genomes]
rs1259354	0.91[ASN][1000 genomes]
rs1259355	0.84[AFR][1000 genomes]
rs1259356	0.98[ASN][1000 genomes]
rs1259359	0.98[ASN][1000 genomes]
rs1259386	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259389	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1259405	0.98[ASN][1000 genomes]
rs1259409	0.84[ASN][1000 genomes]
rs1259426	0.95[ASN][1000 genomes]
rs1259428	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1259435	0.91[ASN][1000 genomes]
rs1259437	0.95[ASN][1000 genomes]
rs1259438	0.91[ASN][1000 genomes]
rs1259441	0.91[ASN][1000 genomes]
rs1262390	0.91[ASN][1000 genomes]
rs1272773	0.91[ASN][1000 genomes]
rs1542536	0.89[ASN][1000 genomes]
rs1677186	0.98[ASN][1000 genomes]
rs1677187	0.98[ASN][1000 genomes]
rs1716194	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2061761	0.98[ASN][1000 genomes]
rs2568884	0.81[AFR][1000 genomes]
rs2568885	0.81[ASN][1000 genomes]
rs2568887	0.86[ASN][1000 genomes]
rs2617178	0.91[ASN][1000 genomes]
rs2617190	0.85[AFR][1000 genomes]
rs2617191	0.84[ASN][1000 genomes]
rs2682671	0.86[ASN][1000 genomes]
rs2682674	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2682677	0.84[ASN][1000 genomes]
rs2682679	0.84[ASN][1000 genomes]
rs2682680	0.81[ASN][1000 genomes]
rs2682695	0.86[ASN][1000 genomes]
rs2682697	0.85[AFR][1000 genomes]
rs35906870	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3898368	0.81[AMR][1000 genomes]
rs4312145	0.89[ASN][1000 genomes]
rs708200	0.83[EUR][1000 genomes]
rs71440988	0.80[AFR][1000 genomes]
rs793146	0.83[AFR][1000 genomes]
rs793148	0.86[ASN][1000 genomes]
rs793149	0.86[ASN][1000 genomes]
rs793150	0.83[ASN][1000 genomes]
rs793173	0.91[ASN][1000 genomes]
rs793174	0.91[ASN][1000 genomes]
rs793175	0.88[ASN][1000 genomes]
rs793177	0.91[ASN][1000 genomes]
rs793180	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs793184	0.85[AFR][1000 genomes]
rs793186	0.84[ASN][1000 genomes]
rs809407	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs899159	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976874	0.91[ASN][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	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
4	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
5	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
6	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
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv52934	chr12:31721932-31731107	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31719000-31731200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:31720000-31731400	Weak transcription	Brain Germinal Matrix	brain
3	chr12:31721600-31742400	Weak transcription	Aorta	Aorta
4	chr12:31722200-31731000	Weak transcription	HSMM	muscle
5	chr12:31722800-31730800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:31722800-31735200	Weak transcription	Spleen	Spleen
7	chr12:31723800-31731400	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:31724000-31730800	Weak transcription	HSMMtube	muscle
9	chr12:31724200-31730800	Weak transcription	Pancreas	Pancrea
10	chr12:31724200-31730800	Weak transcription	Right Atrium	heart
11	chr12:31724200-31731000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:31724200-31731200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:31724200-31731400	Weak transcription	Fetal Kidney	kidney
14	chr12:31724200-31731600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:31726200-31731200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:31726400-31742000	Weak transcription	Fetal Intestine Large	intestine
17	chr12:31726600-31732400	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:31726600-31738000	Weak transcription	Liver	Liver
19	chr12:31727000-31731200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:31727000-31731600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:31727000-31733400	Weak transcription	Ovary	ovary
22	chr12:31727000-31738000	Weak transcription	Small Intestine	intestine
23	chr12:31727400-31729000	Enhancers	Primary hematopoietic stem cells	blood
24	chr12:31727400-31729200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:31727600-31729000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:31727800-31729000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:31727800-31730800	Enhancers	Primary B cells from cord blood	blood
28	chr12:31727800-31737200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:31728000-31730800	Weak transcription	Brain Anterior Caudate	brain
30	chr12:31728000-31730800	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:31728000-31731200	Weak transcription	Adipose Nuclei	Adipose
32	chr12:31728000-31731400	Weak transcription	Fetal Lung	lung
33	chr12:31728000-31741000	Weak transcription	Right Ventricle	heart
34	chr12:31728200-31730800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:31728200-31731000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:31728200-31731200	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:31728200-31738000	Weak transcription	Hela-S3	cervix
38	chr12:31728400-31731200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:31728400-31731200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:31728400-31731200	Weak transcription	Brain Substantia Nigra	brain
41	chr12:31728400-31731200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:31728400-31731200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:31728400-31731200	Enhancers	GM12878-XiMat	blood
44	chr12:31728400-31731200	Weak transcription	NHDF-Ad	bronchial
45	chr12:31728400-31731400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:31728400-31731600	Weak transcription	NHLF	lung
47	chr12:31728400-31731800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:31728400-31732200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:31728400-31734600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:31728400-31741800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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