Variant report

Variant	rs6723733
Chromosome Location	chr2:10442541-10442542
allele	C/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	chr2:10441852-10444651	Hela-S3	cervix:	n/a	n/a
2	ZNF143	chr2:10442515-10443615	GM12878	blood:	n/a	chr2:10443144-10443154
3	ZBTB7A	chr2:10442413-10443103	K562	blood:	n/a	n/a
4	POLR2A	chr2:10442386-10443406	PFSK-1	brain:	n/a	n/a
5	CTCF	chr2:10442461-10442930	HepG2	liver:	n/a	chr2:10442477-10442485
6	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
7	FOXP2	chr2:10442393-10442912	PFSK-1	brain:	n/a	n/a
8	TCF12	chr2:10442450-10442908	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:10442406-10443312	NB4	blood:	n/a	n/a
10	SIN3AK20	chr2:10442357-10444464	MCF-7	breast:	n/a	n/a
11	JUND	chr2:10442423-10443317	A549	lung:	n/a	n/a
12	POLR2A	chr2:10442365-10443189	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:10442419-10443271	K562	blood:	n/a	n/a
14	ELF1	chr2:10442452-10442869	HepG2	liver:	n/a	chr2:10442857-10442869 chr2:10442632-10442645
15	POLR2A	chr2:10441735-10443554	K562	blood:	n/a	n/a
16	POLR2A	chr2:10442473-10443286	HEK293	kidney:	n/a	n/a
17	EGR1	chr2:10442455-10443147	K562	blood:	n/a	chr2:10442644-10442658 chr2:10442633-10442642
18	POLR2A	chr2:10442450-10443381	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr2:10442398-10443255	K562	blood:	n/a	n/a
20	HDAC2	chr2:10441303-10443996	HepG2	liver:	n/a	chr2:10443666-10443685
21	SPI1	chr2:10442410-10442897	HL-60	blood:	n/a	chr2:10442606-10442619
22	ZC3H11A	chr2:10442382-10442845	K562	blood:	n/a	n/a
23	POLR2A	chr2:10442358-10443324	GM10847	blood:	n/a	n/a
24	POLR2A	chr2:10442538-10442575	H1-hESC	embryonic stem cell:	n/a	n/a
25	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
26	POLR2A	chr2:10442226-10444098	MCF-7	breast:	n/a	n/a
27	GABPA	chr2:10442337-10443178	MCF-7	breast:	n/a	n/a
28	POLR2A	chr2:10442372-10443254	GM15510	blood:	n/a	n/a
29	RAD21	chr2:10442480-10443050	ECC-1	luminal epithelium:	n/a	n/a
30	EGR1	chr2:10442407-10443137	K562	blood:	n/a	chr2:10442644-10442658 chr2:10442633-10442642
31	POLR2A	chr2:10442450-10442904	A549	lung:	n/a	n/a
32	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
33	CTCF	chr2:10442452-10443064	MCF-7	breast:	n/a	chr2:10442477-10442485
34	POLR2A	chr2:10442363-10442640	MCF-7	breast:	n/a	n/a
35	POLR2A	chr2:10442492-10442893	PANC-1	pancreas:	n/a	n/a
36	ZBTB7A	chr2:10442419-10443080	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr2:10442377-10443208	K562	blood:	n/a	n/a
38	ZBTB7A	chr2:10442473-10443005	HepG2	liver:	n/a	n/a
39	HNF4A	chr2:10442540-10442994	HepG2	liver:	n/a	chr2:10442717-10442729 chr2:10442714-10442732 chr2:10442719-10442741 chr2:10442715-10442730 chr2:10442723-10442737 chr2:10442717-10442729 chr2:10442717-10442729 chr2:10442717-10442730
40	POLR2A	chr2:10442482-10443385	U87	brain:	n/a	n/a
41	CREB1	chr2:10442443-10443528	A549	lung:	n/a	n/a
42	YY1	chr2:10442538-10442825	H1-hESC	embryonic stem cell:	n/a	n/a
43	MXI1	chr2:10442433-10444519	GM12878	blood:	n/a	chr2:10443806-10443815 chr2:10443808-10443817
44	EP300	chr2:10442408-10443500	ECC-1	luminal epithelium:	n/a	chr2:10443430-10443443 chr2:10443150-10443166
45	POLR2A	chr2:10441906-10443455	Raji	blood:	n/a	n/a
46	MYBL2	chr2:10441021-10443695	HepG2	liver:	n/a	n/a
47	NR3C1	chr2:10442325-10443545	A549	lung:	n/a	n/a
48	POLR2A	chr2:10442503-10443410	HUVEC	blood vessel:	n/a	n/a
49	SPI1	chr2:10442525-10442827	HL-60	blood:	n/a	chr2:10442606-10442619
50	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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:10442521-10442571	GM12878	blood:	n/a
2	chr2:10442521-10442571	AoSMC	blood vessel:	n/a
3	chr2:10442521-10442571	HepG2	liver:	n/a
4	chr2:10442521-10442571	ProgFib	skin:	n/a
5	chr2:10442521-10442571	ECC-1	luminal epithelium:	n/a
6	chr2:10442521-10442571	GM12892	blood:	n/a
7	chr2:10442521-10442571	HUVEC	blood vessel:	n/a
8	chr2:10442521-10442571	LNCaP	prostate:	n/a
9	chr2:10442521-10442571	K562	blood:	n/a
10	chr2:10442521-10442571	HRPEpiC	eye:	n/a
11	chr2:10442521-10442571	HNPCEpiC	eye:	n/a
12	chr2:10442521-10442571	SAEC	small airway:	n/a
13	chr2:10442521-10442571	ovcar-3	ovarian:	n/a
14	chr2:10442521-10442571	SKMC	muscle:	n/a
15	chr2:10442521-10442571	U87	brain:	n/a
16	chr2:10442521-10442571	A549	lung:	n/a
17	chr2:10442521-10442571	BE2_C	brain:	n/a
18	chr2:10442521-10442571	H1-hESC	embryonic stem cell:	embryo
19	chr2:10442521-10442571	SK-N-MC	brain:	n/a
20	chr2:10442521-10442571	BJ	skin:	n/a
21	chr2:10442521-10442571	Caco-2	colon:	n/a
22	chr2:10442521-10442571	AG04449	skin:	fetal
23	chr2:10442521-10442571	MCF-7	breast:	n/a
24	chr2:10442521-10442571	NH-A	brain:	n/a
25	chr2:10442521-10442571	HCM	heart:	n/a
26	chr2:10442521-10442571	NT2-D1	testis:	n/a
27	chr2:10442521-10442571	HMEC	breast:	n/a
28	chr2:10442521-10442571	NB4	blood:	n/a
29	chr2:10442521-10442571	RPTEC	kidney:	n/a
30	chr2:10442521-10442571	Jurkat	blood:	n/a
31	chr2:10442521-10442571	SK-N-SH	brain:	n/a
32	chr2:10442521-10442571	CMK	blood:	n/a
33	chr2:10442521-10442571	Hepatocyte	liver:	n/a
34	chr2:10442521-10442571	AG09309	skin:	n/a
35	chr2:10442521-10442571	HEK293	kidney:	embryo
36	chr2:10442521-10442571	NHBE	bronchial:	n/a
37	chr2:10442521-10442571	MCF10A-Er-Src	breast:	n/a
38	chr2:10442521-10442571	HAEpiC	amniotic membrane:	n/a
39	chr2:10442521-10442571	PrEC	prostate:	n/a
40	chr2:10442521-10442571	HRE	kidney:	n/a
41	chr2:10442521-10442571	AG10803	skin:	n/a
42	chr2:10442521-10442571	SK-N-SH_RA	brain:	n/a
43	chr2:10442521-10442571	GM19239	blood:	n/a
44	chr2:10442521-10442571	PANC-1	pancreas:	n/a
45	chr2:10442521-10442571	GM12891	blood:	n/a
46	chr2:10442521-10442571	AG04450	lung:	fetal
47	chr2:10442521-10442571	HEEpiC	esophagus:	n/a
48	chr2:10442521-10442571	Hela-S3	cervix:	n/a
49	chr2:10442521-10442571	HCPEpiC	choroid plexus:	n/a
50	chr2:10442521-10442571	HRCEpiC	kidney:	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
HPCAL1	CpG island
ENSG00000115758	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000166323	Chromatin interaction
ENSG00000264030	Chromatin interaction
ENSG00000206898	Chromatin interaction
ENSG00000172059	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000171848	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12990770	0.84[AMR][1000 genomes]
rs6714483	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv10180	chr2:10442471-10443799	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription 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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10438800-10442600	Weak transcription	NHLF	lung
2	chr2:10441000-10442600	Enhancers	Stomach Mucosa	stomach
3	chr2:10441200-10442600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr2:10441400-10442600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr2:10441400-10442600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr2:10441400-10442600	Flanking Active TSS	Fetal Intestine Small	intestine
7	chr2:10441600-10442600	Flanking Active TSS	Fetal Intestine Large	intestine
8	chr2:10441600-10442600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr2:10441600-10442600	Enhancers	Spleen	Spleen
10	chr2:10441600-10442800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:10441600-10444800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:10441800-10442600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr2:10441800-10442600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr2:10441800-10442600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr2:10441800-10442600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:10441800-10442600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:10441800-10442600	Flanking Active TSS	Colonic Mucosa	Colon
18	chr2:10441800-10442600	Flanking Active TSS	GM12878-XiMat	blood
19	chr2:10441800-10442600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr2:10441800-10443800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr2:10441800-10445600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:10442000-10442600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:10442000-10442600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr2:10442000-10442600	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr2:10442000-10442600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:10442000-10442600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:10442000-10442600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:10442000-10442600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:10442000-10442600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:10442000-10442600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
31	chr2:10442000-10442800	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr2:10442000-10442800	Enhancers	Fetal Brain Male	brain
33	chr2:10442000-10443200	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr2:10442000-10443200	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr2:10442000-10443600	Active TSS	Rectal Smooth Muscle	rectum
36	chr2:10442000-10444000	Active TSS	Liver	Liver
37	chr2:10442200-10442600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
38	chr2:10442200-10442600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:10442200-10442600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:10442200-10442600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:10442200-10442600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:10442200-10442600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr2:10442200-10442600	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr2:10442200-10442600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:10442200-10442600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:10442200-10442600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr2:10442200-10442600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:10442200-10442600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:10442200-10442600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:10442200-10442600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links