Variant report

Variant	rs216253
Chromosome Location	chr12:312835-312836
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	MXI1	chr12:312366-313439	SK-N-SH	brain:	n/a	n/a
2	ZBTB7A	chr12:312446-313744	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr12:312825-313380	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr12:312559-313362	ECC-1	luminal epithelium:	n/a	chr12:313111-313119
5	UBTF	chr12:312821-313154	K562	blood:	n/a	n/a
6	BACH1	chr12:312656-312881	H1-hESC	embryonic stem cell:	n/a	n/a
7	HMGN3	chr12:312597-313012	K562	blood:	n/a	n/a
8	E2F6	chr12:312807-313487	A549	lung:	n/a	chr12:313047-313059
9	ZBTB7A	chr12:312349-313337	ECC-1	luminal epithelium:	n/a	n/a
10	SIN3A	chr12:312704-313315	H1-hESC	embryonic stem cell:	n/a	chr12:313295-313306 chr12:313041-313052
11	MAX	chr12:312541-313512	A549	lung:	n/a	n/a
12	MAX	chr12:312593-313515	ECC-1	luminal epithelium:	n/a	n/a
13	CREB1	chr12:312552-312913	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:311759..314778-chr12:317325..320101,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IQSEC3-2	chr12:312808-312905	ENSG00000256577.1

Variant related genes	Relation type
SLC6A12	TF binding region
ENSG00000111181	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs188610	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv983433	chr12:145740-400932	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv427901	chr12:146333-344299	Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv428269	chr12:146333-344299	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1038621	chr12:150430-324923	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1047614	chr12:282465-316360	Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv556856	chr12:282465-327421	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv468946	chr12:282465-335922	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv556855	chr12:282465-335922	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv898561	chr12:282465-335922	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1051166	chr12:282465-341144	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv898560	chr12:282465-349298	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv898557	chr12:282465-367902	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv491944	chr12:282465-369192	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv468947	chr12:282465-377904	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv556857	chr12:282465-377904	Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv1037090	chr12:282465-387718	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv1042229	chr12:282465-387718	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv541303	chr12:282465-387718	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv1046121	chr12:282465-416134	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	nsv531957	chr12:282465-465789	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	nsv1049579	chr12:282465-471163	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
22	nsv949498	chr12:282465-493900	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv1051726	chr12:282465-511843	Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
24	nsv541304	chr12:282465-635505	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
25	nsv1042991	chr12:282465-666255	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
26	nsv1041574	chr12:282465-812000	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong 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	40 gene(s)	inside rSNPs	diseases
27	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
28	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
29	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
30	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
31	nsv898562	chr12:285110-318366	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
32	nsv556861	chr12:293513-360614	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
33	nsv1036580	chr12:295971-365820	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
34	nsv1054973	chr12:296179-464439	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
35	nsv541321	chr12:296179-464439	Weak transcription Strong transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
36	nsv523142	chr12:299043-332860	Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:298800-313200	Weak transcription	Gastric	stomach
2	chr12:300000-317200	Strong transcription	Liver	Liver
3	chr12:311000-313400	Enhancers	Placenta	Placenta
4	chr12:311200-313200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:312200-313800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr12:312400-313000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:312400-313000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:312400-313000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
9	chr12:312400-313000	Active TSS	Brain Germinal Matrix	brain
10	chr12:312400-313000	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr12:312400-313200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr12:312400-313200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:312400-313200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:312400-313200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:312400-313200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:312400-313200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:312400-313200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr12:312400-313200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:312400-313200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:312400-313200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
21	chr12:312400-313200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:312400-313200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:312400-313200	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr12:312400-313200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:312400-313200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
26	chr12:312400-313200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
27	chr12:312400-313200	Bivalent/Poised TSS	Fetal Stomach	stomach
28	chr12:312400-313200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
29	chr12:312400-313200	Active TSS	A549	lung
30	chr12:312400-313400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:312400-313400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:312400-313400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:312400-313400	Bivalent/Poised TSS	Fetal Brain Female	brain
34	chr12:312400-313400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr12:312400-313600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr12:312400-313600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:312400-313600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:312400-313800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr12:312400-314000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr12:312600-313000	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:312600-313000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:312600-313000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:312600-313000	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr12:312600-313000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:312600-313000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
46	chr12:312600-313000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:312600-313000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:312600-313000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr12:312600-313000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
50	chr12:312600-313000	Active TSS	Left Ventricle	heart

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