Variant report

Variant	rs2271219
Chromosome Location	chr5:98108649-98108650
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	GATA2	chr5:98108248-98110520	SH-SY5Y	brain:	n/a	chr5:98109257-98109267
2	SIN3AK20	chr5:98108522-98110761	SK-N-SH	brain:	n/a	n/a
3	GABPA	chr5:98108477-98109459	MCF-7	breast:	n/a	chr5:98109181-98109190
4	POLR2A	chr5:98108546-98109603	SK-N-SH	brain:	n/a	n/a
5	MAX	chr5:98108503-98109661	SK-N-SH	brain:	n/a	chr5:98109181-98109191
6	SIN3AK20	chr5:98108444-98108812	H1-hESC	embryonic stem cell:	n/a	n/a
7	CREB1	chr5:98108513-98110448	GM12878	blood:	n/a	n/a
8	TCF12	chr5:98108409-98110611	A549	lung:	n/a	chr5:98110256-98110265
9	POLR2A	chr5:98108580-98109715	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr5:98108598-98110530	ECC-1	luminal epithelium:	n/a	chr5:98110256-98110265
11	MAX	chr5:98108437-98110865	HepG2	liver:	n/a	chr5:98109181-98109191
12	TEAD4	chr5:98108516-98108906	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr5:98108607-98108869	HCT-116	colon:	n/a	n/a
14	CREB1	chr5:98108552-98109792	H1-hESC	embryonic stem cell:	n/a	n/a
15	CREB1	chr5:98108589-98109801	A549	lung:	n/a	n/a
16	SP1	chr5:98108640-98109632	GM12878	blood:	n/a	chr5:98109521-98109528 chr5:98109315-98109324 chr5:98109516-98109530 chr5:98109313-98109325 chr5:98109313-98109325 chr5:98109308-98109320 chr5:98109308-98109320 chr5:98109246-98109267 chr5:98109310-98109319
17	POLR2A	chr5:98108625-98110318	GM15510	blood:	n/a	n/a
18	MAZ	chr5:98108020-98110605	IMR90	lung:	n/a	chr5:98109181-98109191
19	MAX	chr5:98108320-98110731	HCT-116	colon:	n/a	chr5:98109181-98109191
20	TBP	chr5:98108587-98109747	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr5:98108473-98109656	PANC-1	pancreas:	n/a	n/a
22	MAX	chr5:98108518-98110763	MCF-7	breast:	n/a	chr5:98109181-98109191
23	POLR2A	chr5:98107933-98109677	SK-N-SH	brain:	n/a	n/a
24	JUND	chr5:98108615-98108832	H1-hESC	embryonic stem cell:	n/a	n/a
25	CREB1	chr5:98108614-98109781	H1-hESC	embryonic stem cell:	n/a	n/a
26	SIN3AK20	chr5:98108545-98109160	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr5:98108523-98110482	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:98108421-98110443	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr5:98108408-98109836	HUVEC	blood vessel:	n/a	n/a
30	MAX	chr5:98108627-98110737	GM12878	blood:	n/a	chr5:98109181-98109191
31	ELF1	chr5:98108548-98110605	GM12878	blood:	n/a	chr5:98109539-98109548 chr5:98109449-98109461 chr5:98109535-98109547
32	HCFC1	chr5:98108112-98110714	Hela-S3	cervix:	n/a	n/a
33	CREB1	chr5:98108552-98109572	HepG2	liver:	n/a	n/a
34	E2F6	chr5:98108284-98110633	A549	lung:	n/a	chr5:98109353-98109363 chr5:98108835-98108844 chr5:98109181-98109190 chr5:98109594-98109604 chr5:98109574-98109584
35	POLR2A	chr5:98108575-98110513	GM12892	blood:	n/a	n/a
36	ELF1	chr5:98108542-98109521	MCF-7	breast:	n/a	chr5:98109449-98109461
37	POLR2A	chr5:98108489-98110447	HUVEC	blood vessel:	n/a	n/a
38	RCOR1	chr5:98108644-98110612	Hela-S3	cervix:	n/a	n/a
39	REST	chr5:98108616-98109287	A549	lung:	n/a	n/a
40	MYC	chr5:98108396-98110663	A549	lung:	n/a	chr5:98109181-98109191
41	PBX3	chr5:98108594-98109814	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr5:98108649-98109721	Hela-S3	cervix:	n/a	n/a
43	SP1	chr5:98108437-98109820	HCT-116	colon:	n/a	chr5:98109521-98109528 chr5:98109315-98109324 chr5:98109516-98109530 chr5:98109313-98109325 chr5:98109313-98109325 chr5:98109308-98109320 chr5:98109308-98109320 chr5:98109246-98109267 chr5:98109310-98109319
44	SP1	chr5:98108626-98109569	H1-hESC	embryonic stem cell:	n/a	chr5:98109521-98109528 chr5:98109315-98109324 chr5:98109516-98109530 chr5:98109313-98109325 chr5:98109313-98109325 chr5:98109308-98109320 chr5:98109308-98109320 chr5:98109246-98109267 chr5:98109310-98109319
45	MAX	chr5:98108586-98109788	H1-hESC	embryonic stem cell:	n/a	chr5:98109181-98109191
46	TEAD4	chr5:98108494-98108916	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr5:98108583-98110401	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr5:98108531-98109684	GM12891	blood:	n/a	n/a
49	POLR2A	chr5:98108595-98110320	HUVEC	blood vessel:	n/a	n/a
50	MAX	chr5:98108511-98109865	SK-N-SH	brain:	n/a	chr5:98109181-98109191

No.	Distal block	Cell Line	Cell type
1	chr5:98103871..98107404-chr5:98108128..98112327,8	MCF-7	breast:
2	chr5:98102131..98106489-chr5:98107320..98111501,11	MCF-7	breast:
3	chr17:59476329..59477978-chr5:98107765..98110191,2	MCF-7	breast:
4	chr5:96517103..96519459-chr5:98107837..98111064,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHD1-1	chr5:98108326-98108792	ENSG00000246763.2
2	lnc-CHD1-1	chr5:98108326-98108788	NR_033932
3	lnc-CHD1-1	chr5:98108326-98108780	NONHSAT102949
4	lnc-CTD-2215E18.1.1-7	chr5:98108646-98108679	NONHSAT102948

Variant related genes	Relation type
RGMB-AS1	TF binding region
RGMB	TF binding region
ENSG00000121068	Chromatin interaction
ENSG00000058729	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000251513	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000174136	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2662255	1.00[CHD][hapmap]
rs55859771	0.86[ASN][1000 genomes]
rs59860217	0.86[ASN][1000 genomes]
rs73773553	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv3339628	chr5:98107452-98111750	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	esv3394593	chr5:98108277-98110825	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98103800-98112600	Active TSS	Rectal Smooth Muscle	rectum
2	chr5:98104000-98111400	Active TSS	Psoas Muscle	Psoas
3	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:98104200-98111600	Active TSS	Right Atrium	heart
5	chr5:98104400-98109800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:98104400-98110800	Active TSS	HSMMtube	muscle
7	chr5:98105200-98109400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:98106000-98108800	Weak transcription	Spleen	Spleen
9	chr5:98106400-98108800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:98106400-98108800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:98106400-98108800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
12	chr5:98106400-98109400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:98106600-98108800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:98106600-98108800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:98107400-98108800	Flanking Active TSS	HUVEC	blood vessel
16	chr5:98107400-98109600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:98107600-98108800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:98107600-98108800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:98107600-98108800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr5:98107600-98108800	Flanking Active TSS	NH-A	brain
21	chr5:98107800-98108800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:98107800-98108800	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr5:98107800-98108800	Flanking Active TSS	NHEK	skin
24	chr5:98108000-98108800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr5:98108000-98108800	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr5:98108000-98108800	Flanking Active TSS	Stomach Mucosa	stomach
27	chr5:98108000-98108800	Flanking Active TSS	HMEC	breast
28	chr5:98108200-98108800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr5:98108200-98108800	Flanking Active TSS	Liver	Liver
30	chr5:98108200-98108800	Flanking Active TSS	Fetal Intestine Large	intestine
31	chr5:98108200-98108800	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr5:98108200-98108800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr5:98108200-98108800	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr5:98108200-98108800	Flanking Active TSS	GM12878-XiMat	blood
35	chr5:98108200-98108800	Transcr. at gene 5' and 3'	NHLF	lung
36	chr5:98108200-98109200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr5:98108200-98109200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr5:98108200-98109400	Active TSS	Gastric	stomach
39	chr5:98108200-98111000	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr5:98108200-98111000	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr5:98108200-98111000	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr5:98108200-98112200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:98108200-98112400	Active TSS	Colonic Mucosa	Colon
44	chr5:98108400-98108800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr5:98108400-98108800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
46	chr5:98108400-98108800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
47	chr5:98108400-98108800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
48	chr5:98108400-98108800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:98108400-98108800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
50	chr5:98108400-98108800	Flanking Active TSS	Right Ventricle	heart

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