Variant report

Variant	rs12298887
Chromosome Location	chr12:25356709-25356710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:25346979..25351038-chr12:25351626..25357714,8	K562	blood:
2	chr12:25355467..25357313-chr12:25364708..25367209,2	MCF-7	breast:
3	chr12:25356292..25358617-chr12:25386148..25388337,2	K562	blood:

Variant related genes	Relation type
ENSG00000205707	Chromatin interaction
ENSG00000118307	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11047871	0.84[YRI][hapmap]
rs11047872	0.84[YRI][hapmap]
rs12099691	1.00[MEX][hapmap]
rs12299793	0.81[AMR][1000 genomes]
rs12310501	0.82[AMR][1000 genomes]
rs7304274	0.92[YRI][hapmap]
rs7953861	0.84[YRI][hapmap]
rs7972282	0.87[ASW][hapmap];0.88[LWK][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1048631	chr12:25353517-25378661	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25360000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
4	chr12:25348800-25359400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:25348800-25360200	Weak transcription	Esophagus	oesophagus
6	chr12:25349000-25357600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:25349000-25360000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:25349000-25360000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:25349000-25360400	Weak transcription	Psoas Muscle	Psoas
10	chr12:25349000-25369200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:25349000-25372800	Weak transcription	Aorta	Aorta
12	chr12:25349000-25374200	Weak transcription	Lung	lung
13	chr12:25349000-25386000	Weak transcription	Left Ventricle	heart
14	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
15	chr12:25349200-25359000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:25349200-25359400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:25349200-25360800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:25349200-25362400	Weak transcription	Colonic Mucosa	Colon
19	chr12:25349200-25363200	Weak transcription	Brain Substantia Nigra	brain
20	chr12:25349200-25363400	Weak transcription	Stomach Mucosa	stomach
21	chr12:25349400-25357200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:25349400-25357600	Weak transcription	Adipose Nuclei	Adipose
23	chr12:25349400-25359800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:25349400-25367400	Weak transcription	Fetal Stomach	stomach
25	chr12:25349400-25388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:25349400-25388600	Weak transcription	NHLF	lung
27	chr12:25349400-25393800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr12:25349400-25396000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:25349400-25401800	Weak transcription	Fetal Brain Male	brain
30	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
31	chr12:25349600-25356800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:25349600-25358400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:25349600-25359200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:25349600-25359200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:25349600-25359400	Weak transcription	Fetal Kidney	kidney
36	chr12:25349600-25359400	Weak transcription	Fetal Lung	lung
37	chr12:25349600-25360000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:25349600-25360000	Weak transcription	Fetal Brain Female	brain
39	chr12:25349600-25360800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:25349600-25364600	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:25349600-25389000	Weak transcription	Brain Angular Gyrus	brain
42	chr12:25349600-25394600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:25349800-25358000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:25349800-25358400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:25349800-25359800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:25349800-25360000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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