Variant report

Variant	rs238530
Chromosome Location	chr12:58135659-58135660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr12:58135558-58136187	GM12878	blood:	n/a	chr12:58135993-58136006
2	NR2F2	chr12:58135067-58136252	MCF-7	breast:	n/a	n/a
3	POLR2A	chr12:58135653-58136341	HCT-116	colon:	n/a	n/a
4	RUNX3	chr12:58135608-58136221	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:58135591-58136306	GM12892	blood:	n/a	n/a
6	STAT5A	chr12:58135442-58135951	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:58135650-58136248	GM12878	blood:	n/a	n/a
8	MAZ	chr12:58135633-58136200	GM12878	blood:	n/a	n/a
9	MYC	chr12:58135322-58136310	NB4	blood:	n/a	n/a
10	MTA3	chr12:58135483-58136450	GM12878	blood:	n/a	n/a
11	MAX	chr12:58135517-58136303	MCF-7	breast:	n/a	n/a
12	POLR2A	chr12:58135564-58136315	Raji	blood:	n/a	n/a
13	EBF1	chr12:58135351-58136274	GM12878	blood:	n/a	n/a
14	WRNIP1	chr12:58134763-58136381	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:58134720-58136328	GM12891	blood:	n/a	n/a
16	POLR2A	chr12:58135624-58136280	GM12878	blood:	n/a	n/a
17	EP300	chr12:58135452-58135710	GM12878	blood:	n/a	n/a
18	RUNX3	chr12:58135648-58136397	GM12878	blood:	n/a	n/a
19	ZNF217	chr12:58135546-58136135	MCF-7	breast:	n/a	n/a
20	ELF1	chr12:58135468-58136286	MCF-7	breast:	n/a	chr12:58135993-58136006

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58021553..58023386-chr12:58135424..58137328,2	K562	blood:
2	chr12:57912826..57917389-chr12:58135038..58139778,7	K562	blood:
3	chr12:58133058..58135797-chr12:58239105..58241667,3	MCF-7	breast:
4	chr12:57915284..57917737-chr12:58135302..58137824,2	K562	blood:
5	chr12:58087963..58090015-chr12:58135422..58139186,3	K562	blood:

No data

Variant related genes	Relation type
AGAP2	TF binding region
TSPAN31	TF binding region
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000135454	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1871415	1.00[AMR][1000 genomes]
rs2372489	1.00[AMR][1000 genomes]
rs238524	1.00[YRI][hapmap]
rs238525	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs238526	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs238529	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7976556	1.00[YRI][hapmap]
rs937540	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	nsv826386	chr12:58135303-58150535	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 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	chr12:58133200-58135800	Weak transcription	Right Atrium	heart
5	chr12:58133200-58138000	Weak transcription	Pancreas	Pancrea
6	chr12:58133600-58136400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr12:58133800-58136400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:58133800-58137800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:58133800-58138000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:58134000-58136400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr12:58134200-58136200	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr12:58134200-58136400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr12:58134200-58136400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:58134200-58136400	Flanking Active TSS	Dnd41	blood
15	chr12:58134200-58136600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr12:58134200-58136600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr12:58134400-58136000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:58134400-58136000	Flanking Active TSS	Fetal Thymus	thymus
19	chr12:58134400-58136400	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr12:58134400-58138000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:58134600-58136000	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr12:58134600-58136400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr12:58134800-58135800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
24	chr12:58134800-58136000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:58134800-58136000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:58134800-58136000	Active TSS	Rectal Smooth Muscle	rectum
27	chr12:58134800-58136200	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr12:58134800-58138000	Weak transcription	Brain Angular Gyrus	brain
29	chr12:58135000-58135800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr12:58135000-58136000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:58135000-58136400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:58135000-58138000	Weak transcription	Left Ventricle	heart
33	chr12:58135200-58135800	Active TSS	Esophagus	oesophagus
34	chr12:58135200-58135800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
35	chr12:58135200-58136000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr12:58135200-58136000	Active TSS	Liver	Liver
37	chr12:58135200-58136000	Active TSS	Brain Anterior Caudate	brain
38	chr12:58135200-58136000	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr12:58135200-58136000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
40	chr12:58135200-58136000	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
41	chr12:58135200-58137800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:58135200-58137800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:58135200-58138000	Weak transcription	Spleen	Spleen
44	chr12:58135400-58135800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
45	chr12:58135400-58135800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
46	chr12:58135400-58136000	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr12:58135400-58136000	Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr12:58135400-58136000	Active TSS	Adipose Nuclei	Adipose
49	chr12:58135400-58136000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
50	chr12:58135400-58136000	Active TSS	Duodenum Smooth Muscle	Duodenum

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