Variant report

Variant	rs116172975
Chromosome Location	chr2:10442272-10442273
allele	C/T
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	chr2:10441852-10444651	Hela-S3	cervix:	n/a	n/a
2	NFIC	chr2:10441102-10442492	HepG2	liver:	n/a	n/a
3	MYC	chr2:10442125-10444016	A549	lung:	n/a	chr2:10443807-10443817 chr2:10443806-10443816 chr2:10443805-10443814 chr2:10443669-10443678 chr2:10443845-10443854 chr2:10443805-10443820
4	POLR2A	chr2:10441735-10443554	K562	blood:	n/a	n/a
5	HDAC2	chr2:10441303-10443996	HepG2	liver:	n/a	chr2:10443666-10443685
6	RAD21	chr2:10441925-10448398	SK-N-SH	brain:	n/a	chr2:10445901-10445913 chr2:10443150-10443164 chr2:10444235-10444248 chr2:10444579-10444593 chr2:10446784-10446791
7	POLR2A	chr2:10442226-10444098	MCF-7	breast:	n/a	n/a
8	MAX	chr2:10440682-10444624	HepG2	liver:	n/a	chr2:10443807-10443817 chr2:10443806-10443816 chr2:10443805-10443814 chr2:10443669-10443678 chr2:10443845-10443854 chr2:10443805-10443820
9	POLR2A	chr2:10441906-10443455	Raji	blood:	n/a	n/a
10	MYBL2	chr2:10441021-10443695	HepG2	liver:	n/a	n/a
11	FOXA2	chr2:10441946-10442317	HepG2	liver:	n/a	n/a
12	MAZ	chr2:10442124-10445257	IMR90	lung:	n/a	chr2:10443807-10443817 chr2:10443806-10443816 chr2:10443805-10443814 chr2:10443669-10443678 chr2:10443845-10443854 chr2:10443805-10443820
13	POLR2A	chr2:10442222-10442891	HepG2	liver:	n/a	n/a
14	ELF1	chr2:10442099-10443505	GM12878	blood:	n/a	chr2:10442857-10442869 chr2:10442434-10442446 chr2:10442632-10442645
15	JUND	chr2:10442272-10443230	K562	blood:	n/a	n/a
16	CBX3	chr2:10442182-10443186	K562	blood:	n/a	n/a
17	TAF1	chr2:10442122-10444001	HepG2	liver:	n/a	n/a
18	HDAC2	chr2:10442099-10443040	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:10441016-10443943	HepG2	liver:	n/a	n/a
20	MAX	chr2:10442036-10444467	MCF-7	breast:	n/a	chr2:10443807-10443817 chr2:10443806-10443816 chr2:10443805-10443814 chr2:10443669-10443678 chr2:10443845-10443854 chr2:10443805-10443820
21	FOXA1	chr2:10441949-10443219	HepG2	liver:	n/a	n/a
22	CHD2	chr2:10442233-10443171	GM12878	blood:	n/a	n/a
23	GABPA	chr2:10442256-10443084	MCF-7	breast:	n/a	n/a
24	POLR2A	chr2:10441120-10442911	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:10441505-10443270	K562	blood:	n/a	n/a
26	MAX	chr2:10442155-10443245	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr2:10442251-10442869	GM12878	blood:	n/a	n/a
28	MAZ	chr2:10442267-10444414	GM12878	blood:	n/a	chr2:10443807-10443817 chr2:10443806-10443816 chr2:10443805-10443814 chr2:10443669-10443678 chr2:10443845-10443854 chr2:10443805-10443820
29	MAX	chr2:10441745-10444932	A549	lung:	n/a	chr2:10443807-10443817 chr2:10443806-10443816 chr2:10443805-10443814 chr2:10443669-10443678 chr2:10443845-10443854 chr2:10443805-10443820
30	MAX	chr2:10442244-10444508	K562	blood:	n/a	chr2:10443807-10443817 chr2:10443806-10443816 chr2:10443805-10443814 chr2:10443669-10443678 chr2:10443845-10443854 chr2:10443805-10443820
31	CTCF	chr2:10442260-10442410	GM12873	blood:	n/a	n/a
32	MXI1	chr2:10441040-10446748	SK-N-SH	brain:	n/a	chr2:10443806-10443815 chr2:10443808-10443817 chr2:10441998-10442013
33	GABPA	chr2:10442205-10442867	HepG2	liver:	n/a	n/a
34	YY1	chr2:10442118-10443330	HepG2	liver:	n/a	n/a
35	STAT1	chr2:10442228-10443159	GM12878	blood:	n/a	chr2:10442545-10442557
36	MYBL2	chr2:10441007-10443089	HepG2	liver:	n/a	n/a
37	MAX	chr2:10440984-10445011	HepG2	liver:	n/a	chr2:10443807-10443817 chr2:10443806-10443816 chr2:10443805-10443814 chr2:10443669-10443678 chr2:10443845-10443854 chr2:10443805-10443820
38	MAZ	chr2:10442223-10444394	K562	blood:	n/a	chr2:10443807-10443817 chr2:10443806-10443816 chr2:10443805-10443814 chr2:10443669-10443678 chr2:10443845-10443854 chr2:10443805-10443820
39	TAF1	chr2:10442216-10443551	HepG2	liver:	n/a	n/a
40	RCOR1	chr2:10442018-10442888	HepG2	liver:	n/a	n/a
41	POLR2A	chr2:10441113-10442879	HepG2	liver:	n/a	n/a
42	CTCF	chr2:10442037-10444954	A549	lung:	n/a	chr2:10444547-10444556 chr2:10442232-10442241 chr2:10444236-10444249 chr2:10442477-10442485 chr2:10443153-10443166
43	HCFC1	chr2:10442196-10443606	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr2:10441116-10442876	HepG2	liver:	n/a	n/a
45	RUNX3	chr2:10442052-10442429	GM12878	blood:	n/a	chr2:10442139-10442156
46	EP300	chr2:10442116-10443169	HepG2	liver:	n/a	chr2:10443150-10443166
47	MAZ	chr2:10442197-10443597	HepG2	liver:	n/a	n/a
48	HEY1	chr2:10440976-10443359	HepG2	liver:	n/a	chr2:10442577-10442592 chr2:10442848-10442863
49	MXI1	chr2:10442246-10444991	IMR90	lung:	n/a	chr2:10443806-10443815 chr2:10443808-10443817
50	POLR2A	chr2:10442197-10443773	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10424782..10426457-chr2:10440963..10442554,2	K562	blood:
2	chr2:10261055..10262657-chr2:10441629..10443172,2	K562	blood:
3	chr2:10440329..10443014-chr2:10447614..10450153,3	K562	blood:
4	chr2:10259191..10262555-chr2:10441232..10444497,4	K562	blood:
5	chr2:10417267..10421526-chr2:10440124..10444517,8	K562	blood:
6	chr11:108337866..108338745-chr2:10442140..10442929,2	Hela-S3	cervix:
7	chr2:10434745..10440361-chr2:10440769..10446494,13	MCF-7	breast:
8	chr2:10259183..10262149-chr2:10441411..10444855,4	MCF-7	breast:
9	chr2:10441623..10444200-chr2:10586906..10588748,2	K562	blood:
10	chr2:10441262..10442820-chr2:10525916..10527574,2	MCF-7	breast:
11	chr2:10261047..10264754-chr2:10441936..10445688,4	MCF-7	breast:
12	chr2:10417102..10422487-chr2:10439870..10443532,9	K562	blood:
13	chr2:10441623..10444177-chr2:10587166..10588748,2	K562	blood:
14	chr2:10328421..10328930-chr2:10442179..10443004,2	MCF-7	breast:
15	chr2:10265405..10268289-chr2:10440877..10444021,3	K562	blood:
16	chr2:10183111..10185258-chr2:10441327..10442852,2	K562	blood:

Variant related genes	Relation type
HPCAL1	TF binding region
ENSG00000172059	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000206898	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000264030	Chromatin interaction
ENSG00000166323	Chromatin interaction
ENSG00000171848	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873639	chr2:10372061-10475308	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv3356298	chr2:10441526-10444374	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	esv3367929	chr2:10441951-10444149	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10438800-10442600	Weak transcription	NHLF	lung
2	chr2:10439000-10442400	Weak transcription	HSMM	muscle
3	chr2:10439000-10442400	Weak transcription	NH-A	brain
4	chr2:10441000-10442400	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr2:10441000-10442400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr2:10441000-10442600	Enhancers	Stomach Mucosa	stomach
7	chr2:10441200-10442400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr2:10441200-10442600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr2:10441400-10442600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr2:10441400-10442600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr2:10441400-10442600	Flanking Active TSS	Fetal Intestine Small	intestine
12	chr2:10441600-10442400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:10441600-10442400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:10441600-10442400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr2:10441600-10442600	Flanking Active TSS	Fetal Intestine Large	intestine
16	chr2:10441600-10442600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr2:10441600-10442600	Enhancers	Spleen	Spleen
18	chr2:10441600-10442800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:10441600-10444800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:10441800-10442400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:10441800-10442400	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr2:10441800-10442400	Enhancers	Lung	lung
23	chr2:10441800-10442600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr2:10441800-10442600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr2:10441800-10442600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr2:10441800-10442600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:10441800-10442600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:10441800-10442600	Flanking Active TSS	Colonic Mucosa	Colon
29	chr2:10441800-10442600	Flanking Active TSS	GM12878-XiMat	blood
30	chr2:10441800-10442600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr2:10441800-10443800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr2:10441800-10445600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:10442000-10442400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:10442000-10442400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr2:10442000-10442400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr2:10442000-10442400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
37	chr2:10442000-10442400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr2:10442000-10442400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr2:10442000-10442400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr2:10442000-10442400	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr2:10442000-10442400	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr2:10442000-10442400	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr2:10442000-10442400	Enhancers	Colon Smooth Muscle	Colon
44	chr2:10442000-10442400	Enhancers	Small Intestine	intestine
45	chr2:10442000-10442400	Flanking Active TSS	Thymus	Thymus
46	chr2:10442000-10442400	Flanking Active TSS	A549	lung
47	chr2:10442000-10442400	Flanking Active TSS	Hela-S3	cervix
48	chr2:10442000-10442400	Enhancers	HUVEC	blood vessel
49	chr2:10442000-10442400	Flanking Active TSS	K562	blood
50	chr2:10442000-10442600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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