Variant report

Variant	rs238529
Chromosome Location	chr12:58134803-58134804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr12:58134762-58135194	GM12878	blood:	n/a	n/a
2	MXI1	chr12:58134750-58135201	GM12878	blood:	n/a	chr12:58135002-58135017 chr12:58135000-58135015
3	POLR2A	chr12:58134722-58135494	H1-neurons	neurons:	n/a	n/a
4	ZEB1	chr12:58134793-58135226	GM12878	blood:	n/a	n/a
5	TAF1	chr12:58134656-58135078	H1-neurons	neurons:	n/a	n/a
6	REST	chr12:58134418-58135585	H1-neurons	neurons:	n/a	chr12:58135098-58135111
7	RUNX3	chr12:58134752-58135308	GM12878	blood:	n/a	n/a
8	WRNIP1	chr12:58134763-58136381	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:58134720-58136328	GM12891	blood:	n/a	n/a
10	RUNX3	chr12:58134745-58135345	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:58134627-58135485	H1-neurons	neurons:	n/a	n/a
12	TAF1	chr12:58134759-58135232	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57911286..57913384-chr12:58133067..58135116,2	K562	blood:
2	chr12:58133058..58135797-chr12:58239105..58241667,3	MCF-7	breast:

Variant related genes	Relation type
AGAP2	TF binding region
TSPAN31	TF binding region
ENSG00000208028	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1564375	1.00[AMR][1000 genomes]
rs2173633	1.00[AMR][1000 genomes]
rs238524	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs238525	0.89[AFR][1000 genomes]
rs238526	0.89[AFR][1000 genomes]
rs238530	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs35957924	1.00[AMR][1000 genomes]
rs7958927	1.00[AMR][1000 genomes]
rs7976556	1.00[YRI][hapmap]
rs937540	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899122	chr12:58118248-58137563	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
10	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58131200-58138000	Weak transcription	K562	blood
2	chr12:58131800-58138000	Weak transcription	Lung	lung
3	chr12:58132200-58138800	Weak transcription	Gastric	stomach
4	chr12:58133200-58135400	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr12:58133200-58135600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:58133200-58135800	Weak transcription	Right Atrium	heart
7	chr12:58133200-58138000	Weak transcription	Pancreas	Pancrea
8	chr12:58133400-58135400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:58133600-58135200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr12:58133600-58135600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:58133600-58136400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr12:58133800-58135000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:58133800-58135200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:58133800-58136400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:58133800-58137800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:58133800-58138000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:58134000-58135000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr12:58134000-58135000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr12:58134000-58136400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr12:58134200-58135000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:58134200-58135200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:58134200-58135200	Flanking Active TSS	GM12878-XiMat	blood
23	chr12:58134200-58136200	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr12:58134200-58136400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr12:58134200-58136400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:58134200-58136400	Flanking Active TSS	Dnd41	blood
27	chr12:58134200-58136600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr12:58134200-58136600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr12:58134400-58135000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
30	chr12:58134400-58135200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
31	chr12:58134400-58135400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr12:58134400-58135600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr12:58134400-58135600	Flanking Active TSS	Thymus	Thymus
34	chr12:58134400-58136000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:58134400-58136000	Flanking Active TSS	Fetal Thymus	thymus
36	chr12:58134400-58136400	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr12:58134400-58138000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:58134600-58135000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
39	chr12:58134600-58135200	Bivalent Enhancer	Adipose Nuclei	Adipose
40	chr12:58134600-58135200	Enhancers	Liver	Liver
41	chr12:58134600-58135400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
42	chr12:58134600-58135400	Bivalent Enhancer	HUVEC	blood vessel
43	chr12:58134600-58135600	Bivalent/Poised TSS	Colonic Mucosa	Colon
44	chr12:58134600-58136000	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr12:58134600-58136400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr12:58134800-58135000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:58134800-58135200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:58134800-58135200	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr12:58134800-58135200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
50	chr12:58134800-58135200	Enhancers	Spleen	Spleen

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