Variant report

Variant	rs886939
Chromosome Location	chr12:2026690-2026691
allele	A/C
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	POLR2A	chr12:2024578-2028301	PBDE	blood:	n/a	n/a
2	MAX	chr12:2026419-2026743	K562	blood:	n/a	n/a
3	POLR2A	chr12:2026662-2028223	HL-60	blood:	n/a	n/a
4	MAX	chr12:2026360-2028093	NB4	blood:	n/a	chr12:2027897-2027907 chr12:2027887-2027897
5	GATA1	chr12:2024407-2027453	PBDE	blood:	n/a	chr12:2027030-2027047 chr12:2025766-2025775 chr12:2027003-2027013 chr12:2024757-2024767 chr12:2024984-2024992
6	BHLHE40	chr12:2024905-2027201	K562	blood:	n/a	n/a
7	GATA1	chr12:2026674-2027422	K562	blood:	n/a	chr12:2027030-2027047 chr12:2027003-2027013
8	TAL1	chr12:2026623-2027266	K562	blood:	n/a	chr12:2027030-2027048
9	POLR2A	chr12:2025763-2027535	K562	blood:	n/a	n/a
10	MAZ	chr12:2026682-2027291	K562	blood:	n/a	n/a
11	RPC155	chr12:2026027-2027045	K562	blood:	n/a	n/a
12	POLR2A	chr12:2026369-2028390	HL-60	blood:	n/a	n/a
13	MAX	chr12:2026557-2027178	K562	blood:	n/a	n/a
14	GTF3C2	chr12:2026107-2027111	K562	blood:	n/a	n/a
15	RCOR1	chr12:2025588-2027353	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:2023041..2025540-chr12:2026529..2030092,4	K562	blood:

Variant related genes	Relation type
CACNA2D4	TF binding region
ENSG00000256706	TF binding region
ENSG00000151062	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10735005	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11062008	1.00[CHB][hapmap]
rs11062010	1.00[ASN][1000 genomes]
rs12368779	1.00[CHB][hapmap]
rs1558141	1.00[ASN][1000 genomes]
rs1558142	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17801032	1.00[CHB][hapmap]
rs1990232	1.00[ASN][1000 genomes]
rs2008352	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013064	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2429155	1.00[CHB][hapmap]
rs2429158	1.00[ASN][1000 genomes]
rs2429159	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2429163	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2429164	1.00[ASN][1000 genomes]
rs2429167	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429169	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2429184	1.00[ASN][1000 genomes]
rs2470409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470415	0.85[EUR][1000 genomes]
rs2470438	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2470439	1.00[CHB][hapmap]
rs2906892	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs720456	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7315910	1.00[CHB][hapmap]
rs758157	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758158	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181666	1.00[ASN][1000 genomes]
rs8181681	1.00[ASN][1000 genomes]
rs8181786	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs886941	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1046388	chr12:1964846-2034887	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1043329	chr12:1986238-2034887	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv557000	chr12:2008548-2045640	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv898600	chr12:2020045-2056363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2020400-2027000	Enhancers	Fetal Thymus	thymus
2	chr12:2020400-2027400	Enhancers	Fetal Muscle Leg	muscle
3	chr12:2021800-2027400	Weak transcription	Psoas Muscle	Psoas
4	chr12:2022400-2027000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:2022400-2027600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:2022600-2028800	Enhancers	Fetal Heart	heart
7	chr12:2024000-2029000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:2024200-2026800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:2024200-2026800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:2024200-2026800	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr12:2024200-2027200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:2024400-2026800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr12:2024400-2027000	Enhancers	Primary hematopoietic stem cells	blood
14	chr12:2024400-2027200	Enhancers	Primary T cells from cord blood	blood
15	chr12:2024400-2027200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr12:2024400-2027800	Enhancers	Spleen	Spleen
17	chr12:2024600-2026800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:2025000-2026800	Enhancers	Thymus	Thymus
19	chr12:2025000-2027200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr12:2025000-2027200	Enhancers	Placenta	Placenta
21	chr12:2025000-2028000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:2025200-2026800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:2025600-2026800	Enhancers	Primary B cells from cord blood	blood
24	chr12:2025600-2027600	Enhancers	Right Ventricle	heart
25	chr12:2025600-2028400	Enhancers	Right Atrium	heart
26	chr12:2025800-2027200	Enhancers	Left Ventricle	heart
27	chr12:2025800-2027200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr12:2025800-2027600	Bivalent Enhancer	Fetal Stomach	stomach
29	chr12:2025800-2028000	Enhancers	Fetal Lung	lung
30	chr12:2026000-2026800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:2026000-2027000	Enhancers	Brain Hippocampus Middle	brain
32	chr12:2026000-2027000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr12:2026000-2027000	Enhancers	Ovary	ovary
34	chr12:2026000-2027200	Enhancers	Brain Germinal Matrix	brain
35	chr12:2026000-2028800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:2026200-2026800	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr12:2026200-2026800	Enhancers	Brain Anterior Caudate	brain
38	chr12:2026200-2026800	Enhancers	Brain Substantia Nigra	brain
39	chr12:2026200-2027000	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr12:2026200-2027000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr12:2026200-2027000	Enhancers	Stomach Smooth Muscle	stomach
42	chr12:2026200-2027200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr12:2026200-2027600	Enhancers	Liver	Liver
44	chr12:2026200-2027600	Enhancers	Fetal Brain Female	brain
45	chr12:2026400-2027000	Bivalent Enhancer	Adipose Nuclei	Adipose
46	chr12:2026400-2027000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr12:2026400-2027000	Enhancers	Rectal Smooth Muscle	rectum
48	chr12:2026400-2027600	Enhancers	Fetal Brain Male	brain
49	chr12:2026400-2028400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr12:2026400-2028600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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