Variant report

Variant	rs25642
Chromosome Location	chr12:121659917-121659918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:121659907-121659957	A549	lung:	n/a
2	chr12:121659907-121659957	HEK293	kidney:	embryo
3	chr12:121659907-121659957	MCF-7	breast:	n/a
4	chr12:121659907-121659957	U87	brain:	n/a
5	chr12:121659907-121659957	GM12891	blood:	n/a
6	chr12:121659907-121659957	PANC-1	pancreas:	n/a
7	chr12:121659907-121659957	HPAEpiC	pulmonary alveolar:	n/a
8	chr12:121659907-121659957	SK-N-MC	brain:	n/a
9	chr12:121659907-121659957	GM12878	blood:	n/a
10	chr12:121659907-121659957	NH-A	brain:	n/a
11	chr12:121659907-121659957	SAEC	small airway:	n/a
12	chr12:121659907-121659957	BJ	skin:	n/a
13	chr12:121659907-121659957	PFSK-1	brain:	n/a
14	chr12:121659907-121659957	HRCEpiC	kidney:	n/a
15	chr12:121659907-121659957	Jurkat	blood:	n/a
16	chr12:121659907-121659957	RPTEC	kidney:	n/a
17	chr12:121659907-121659957	T-47D	breast:	n/a
18	chr12:121659907-121659957	AG09319	gingival:	n/a
19	chr12:121659907-121659957	NT2-D1	testis:	n/a
20	chr12:121659907-121659957	HEEpiC	esophagus:	n/a
21	chr12:121659907-121659957	GM19239	blood:	n/a
22	chr12:121659907-121659957	GM06990	blood:	n/a
23	chr12:121659907-121659957	MCF10A-Er-Src	breast:	n/a
24	chr12:121659907-121659957	CMK	blood:	n/a
25	chr12:121659907-121659957	ProgFib	skin:	n/a
26	chr12:121659907-121659957	NHBE	bronchial:	n/a
27	chr12:121659907-121659957	HAEpiC	amniotic membrane:	n/a
28	chr12:121659907-121659957	HCT-116	colon:	n/a
29	chr12:121659907-121659957	HRE	kidney:	n/a
30	chr12:121659907-121659957	HCM	heart:	n/a
31	chr12:121659907-121659957	HNPCEpiC	eye:	n/a
32	chr12:121659907-121659957	HepG2	liver:	n/a
33	chr12:121659907-121659957	ovcar-3	ovarian:	n/a
34	chr12:121659907-121659957	LNCaP	prostate:	n/a
35	chr12:121659907-121659957	HIPEpiC	eye:	n/a
36	chr12:121659907-121659957	AG04450	lung:	fetal
37	chr12:121659907-121659957	HL-60	blood:	n/a
38	chr12:121659907-121659957	HRPEpiC	eye:	n/a
39	chr12:121659907-121659957	IMR90	lung:	fetal
40	chr12:121659907-121659957	PrEC	prostate:	n/a
41	chr12:121659907-121659957	HMEC	breast:	n/a
42	chr12:121659907-121659957	SK-N-SH	brain:	n/a
43	chr12:121659907-121659957	ECC-1	luminal epithelium:	n/a
44	chr12:121659907-121659957	K562	blood:	n/a
45	chr12:121659907-121659957	Caco-2	colon:	n/a
46	chr12:121659907-121659957	H1-hESC	embryonic stem cell:	embryo
47	chr12:121659907-121659957	SKMC	muscle:	n/a
48	chr12:121659907-121659957	SK-N-SH_RA	brain:	n/a
49	chr12:121659907-121659957	AG10803	skin:	n/a
50	chr12:121659907-121659957	BE2_C	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121646473..121649457-chr12:121658577..121662737,5	MCF-7	breast:

No data

Variant related genes	Relation type
P2RX4	CpG island
ENSG00000135124	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11065481	0.81[ASN][1000 genomes]
rs1169721	0.81[ASN][1000 genomes]
rs1653586	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1653587	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1653588	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1653589	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1653590	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1653592	0.98[EUR][1000 genomes]
rs1653593	0.98[EUR][1000 genomes]
rs1718118	0.87[EUR][1000 genomes]
rs1718156	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1718158	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2071272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2071273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252298	0.98[EUR][1000 genomes]
rs2252304	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2272076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288691	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2567982	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2668239	0.98[EUR][1000 genomes]
rs2668246	0.98[EUR][1000 genomes]
rs2686339	0.98[EUR][1000 genomes]
rs2686372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28969487	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3751145	1.00[AFR][1000 genomes]
rs3763975	0.86[ASN][1000 genomes]
rs3815990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57379013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57419819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57983015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59037892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60714133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60979871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv899564	chr12:121641509-121689798	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899565	chr12:121641509-121698785	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121648800-121660400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:121648800-121661400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:121648800-121666600	Weak transcription	Ovary	ovary
4	chr12:121649000-121660000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:121649000-121660400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:121649000-121660600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:121649000-121660600	Weak transcription	Brain Germinal Matrix	brain
8	chr12:121649000-121661200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:121649000-121661200	Weak transcription	Esophagus	oesophagus
10	chr12:121649000-121665000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:121649000-121666600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:121649000-121675800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:121649000-121676200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:121649000-121676200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:121649000-121676600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:121649400-121660400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:121649400-121660600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:121649400-121680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:121649600-121660600	Weak transcription	Dnd41	blood
20	chr12:121650000-121660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:121650000-121660800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:121652400-121675600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:121652600-121660600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:121652600-121664800	Weak transcription	Small Intestine	intestine
25	chr12:121652800-121661200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:121653200-121660600	Weak transcription	GM12878-XiMat	blood
27	chr12:121653200-121660800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:121653200-121661200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:121653200-121661200	Weak transcription	K562	blood
30	chr12:121653200-121665000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:121653200-121666400	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:121653200-121675600	Weak transcription	HSMMtube	muscle
33	chr12:121653200-121698800	Weak transcription	Fetal Heart	heart
34	chr12:121653400-121661000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:121653400-121665000	Weak transcription	NHEK	skin
36	chr12:121653400-121673600	Weak transcription	Osteobl	bone
37	chr12:121653400-121677600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:121653400-121678600	Weak transcription	Right Atrium	heart
39	chr12:121653600-121660600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:121653600-121660600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:121653600-121660600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:121653600-121670200	Weak transcription	NHDF-Ad	bronchial
43	chr12:121653800-121660600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:121653800-121660600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:121654200-121660600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:121654600-121660200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr12:121654600-121660200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:121654600-121660400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr12:121654600-121660600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:121654800-121675200	Strong transcription	Fetal Stomach	stomach

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