Variant report

Variant	rs12994169
Chromosome Location	chr2:233924581-233924582
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	POLR2A	chr2:233924233-233929847	GM18505	blood:	n/a	n/a
2	RCOR1	chr2:233924352-233924815	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:233924265-233927493	GM12891	blood:	n/a	n/a
4	POLR2A	chr2:233924311-233930017	GM12891	blood:	n/a	n/a
5	MAX	chr2:233924517-233926909	GM12878	blood:	n/a	chr2:233924691-233924701 chr2:233925175-233925184
6	CTCF	chr2:233924226-233924622	HepG2	liver:	n/a	chr2:233924457-233924475 chr2:233924459-233924472
7	CTCF	chr2:233924346-233924612	GM19239	blood:	n/a	chr2:233924457-233924475 chr2:233924459-233924472
8	RUNX3	chr2:233924334-233927486	GM12878	blood:	n/a	chr2:233926986-233926995
9	RELA	chr2:233924391-233927017	GM15510	blood:	n/a	n/a
10	MAZ	chr2:233924291-233924635	HepG2	liver:	n/a	n/a
11	CTCF	chr2:233924440-233924590	GM12873	blood:	n/a	chr2:233924457-233924475 chr2:233924459-233924472
12	CHD2	chr2:233924376-233925512	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:233924270-233929959	NB4	blood:	n/a	n/a
14	POLR2A	chr2:233924280-233929205	GM15510	blood:	n/a	n/a
15	RAD21	chr2:233924236-233924729	A549	lung:	n/a	chr2:233924466-233924479 chr2:233924458-233924471 chr2:233924455-233924474 chr2:233924597-233924609
16	POLR2A	chr2:233924290-233929787	GM12892	blood:	n/a	n/a
17	CTCF	chr2:233924336-233924608	GM12892	blood:	n/a	chr2:233924457-233924475 chr2:233924459-233924472
18	POLR2A	chr2:233924577-233927554	GM12892	blood:	n/a	n/a
19	ARID3A	chr2:233924409-233924589	HepG2	liver:	n/a	n/a
20	BHLHE40	chr2:233924326-233925570	HepG2	liver:	n/a	chr2:233924458-233924474
21	MXI1	chr2:233924314-233925641	HepG2	liver:	n/a	chr2:233924692-233924701
22	YY1	chr2:233924021-233924815	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:233924284-233925456	HepG2	liver:	n/a	n/a
24	CTCF	chr2:233924268-233924635	H1-hESC	embryonic stem cell:	n/a	chr2:233924457-233924475 chr2:233924459-233924472
25	MYC	chr2:233924250-233925518	NB4	blood:	n/a	chr2:233924691-233924701 chr2:233925175-233925184
26	CHD1	chr2:233924470-233926942	GM12878	blood:	n/a	n/a
27	CTCF	chr2:233924431-233924617	K562	blood:	n/a	chr2:233924457-233924475 chr2:233924459-233924472
28	RAD21	chr2:233924160-233924687	H1-hESC	embryonic stem cell:	n/a	chr2:233924466-233924479 chr2:233924458-233924471 chr2:233924224-233924237 chr2:233924455-233924474 chr2:233924597-233924609
29	MAX	chr2:233924340-233925610	HepG2	liver:	n/a	chr2:233924691-233924701 chr2:233925175-233925184
30	POLR2A	chr2:233924453-233926952	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:233924309-233929170	GM18526	blood:	n/a	n/a
32	CHD2	chr2:233924371-233924757	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:233924579-233927518	GM12878	blood:	n/a	n/a
34	STAT5A	chr2:233924234-233927397	GM12878	blood:	n/a	chr2:233925009-233925020 chr2:233925862-233925869 chr2:233924519-233924531 chr2:233925040-233925047
35	RAD21	chr2:233924257-233924643	H1-hESC	embryonic stem cell:	n/a	chr2:233924466-233924479 chr2:233924458-233924471 chr2:233924455-233924474 chr2:233924597-233924609
36	RAD21	chr2:233924264-233924655	HepG2	liver:	n/a	chr2:233924466-233924479 chr2:233924458-233924471 chr2:233924455-233924474 chr2:233924597-233924609
37	RAD21	chr2:233924282-233924600	GM12878	blood:	n/a	chr2:233924466-233924479 chr2:233924458-233924471 chr2:233924455-233924474
38	ZNF143	chr2:233924318-233925257	GM12878	blood:	n/a	n/a
39	CTCF	chr2:233924270-233925242	GM12878	blood:	n/a	chr2:233924457-233924475 chr2:233924459-233924472
40	RAD21	chr2:233924248-233924675	ECC-1	luminal epithelium:	n/a	chr2:233924466-233924479 chr2:233924458-233924471 chr2:233924455-233924474 chr2:233924597-233924609
41	CTCF	chr2:233924440-233924590	GM12864	blood:	n/a	chr2:233924457-233924475 chr2:233924459-233924472
42	RAD21	chr2:233924121-233924789	HCT-116	colon:	n/a	chr2:233924466-233924479 chr2:233924458-233924471 chr2:233924224-233924237 chr2:233924455-233924474 chr2:233924597-233924609
43	MXI1	chr2:233924428-233929370	GM12878	blood:	n/a	chr2:233924692-233924701 chr2:233928980-233928989 chr2:233926846-233926855
44	RAD21	chr2:233924224-233924662	A549	lung:	n/a	chr2:233924466-233924479 chr2:233924458-233924471 chr2:233924224-233924237 chr2:233924455-233924474 chr2:233924597-233924609
45	POLR2A	chr2:233924327-233925667	HepG2	liver:	n/a	n/a
46	ELF1	chr2:233923748-233927004	GM12878	blood:	n/a	chr2:233925035-233925046 chr2:233924984-233924997 chr2:233925034-233925047
47	RELA	chr2:233924580-233926896	GM18505	blood:	n/a	n/a
48	CTCF	chr2:233924440-233924590	NB4	blood:	n/a	chr2:233924457-233924475 chr2:233924459-233924472
49	POLR2A	chr2:233924344-233926350	HL-60	blood:	n/a	n/a
50	RELA	chr2:233924580-233927117	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
INPP5D	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1141328	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28773607	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28854328	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34218488	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35140857	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4973063	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585583	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876009	chr2:233799400-233996429	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv876012	chr2:233899377-233996429	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233914400-233926600	Weak transcription	HSMMtube	muscle
2	chr2:233916600-233924600	Weak transcription	Pancreas	Pancrea
3	chr2:233917000-233925800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:233917400-233926000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:233919000-233925200	Weak transcription	Brain Angular Gyrus	brain
6	chr2:233919000-233925200	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:233919200-233925200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:233922400-233926200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:233923000-233927800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:233923400-233924800	Weak transcription	Gastric	stomach
11	chr2:233923400-233925000	Enhancers	Spleen	Spleen
12	chr2:233923600-233924600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr2:233923800-233924600	Enhancers	Adipose Nuclei	Adipose
14	chr2:233923800-233924600	Flanking Active TSS	HepG2	liver
15	chr2:233923800-233924800	Enhancers	Primary hematopoietic stem cells	blood
16	chr2:233923800-233924800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr2:233923800-233924800	Enhancers	Right Ventricle	heart
18	chr2:233924000-233924600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr2:233924000-233924600	Enhancers	Brain Anterior Caudate	brain
20	chr2:233924000-233924600	Enhancers	Placenta	Placenta
21	chr2:233924000-233924600	Enhancers	Fetal Thymus	thymus
22	chr2:233924000-233924800	Enhancers	Esophagus	oesophagus
23	chr2:233924000-233924800	Enhancers	Fetal Muscle Trunk	muscle
24	chr2:233924000-233924800	Enhancers	Fetal Muscle Leg	muscle
25	chr2:233924000-233925000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:233924000-233925000	Enhancers	Lung	lung
27	chr2:233924000-233925000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr2:233924200-233924600	Enhancers	Duodenum Mucosa	Duodenum
29	chr2:233924200-233924600	Enhancers	Left Ventricle	heart
30	chr2:233924200-233924600	Enhancers	Stomach Smooth Muscle	stomach
31	chr2:233924200-233924800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr2:233924200-233924800	Weak transcription	Right Atrium	heart
33	chr2:233924200-233924800	Enhancers	HUVEC	blood vessel
34	chr2:233924200-233925000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr2:233924200-233925000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr2:233924200-233925000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr2:233924200-233925000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:233924200-233925000	Enhancers	Fetal Intestine Large	intestine
39	chr2:233924200-233925000	Enhancers	Fetal Intestine Small	intestine
40	chr2:233924200-233925000	Enhancers	Fetal Stomach	stomach
41	chr2:233924200-233925000	Flanking Active TSS	Dnd41	blood
42	chr2:233924200-233925000	Flanking Active TSS	GM12878-XiMat	blood
43	chr2:233924200-233925400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:233924400-233924600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr2:233924400-233924600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:233924400-233924600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr2:233924400-233924600	Enhancers	Stomach Mucosa	stomach
48	chr2:233924400-233924800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:233924400-233924800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr2:233924400-233924800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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