Variant report

Variant	rs11901672
Chromosome Location	chr2:38976925-38976926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:66)
CpG islands
(count:0)
Chromatin interactive
region (count:31)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:66 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr2:38976334-38977429	K562	blood:	n/a	n/a
2	POLR2A	chr2:38976565-38978925	GM12878	blood:	n/a	n/a
3	NFATC1	chr2:38976771-38979006	GM12878	blood:	n/a	chr2:38978665-38978678
4	POLR2A	chr2:38969485-38979320	K562	blood:	n/a	n/a
5	POLR2A	chr2:38973829-38979359	H1-hESC	embryonic stem cell:	n/a	n/a
6	ATF2	chr2:38976904-38977503	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:38973281-38979491	K562	blood:	n/a	n/a
8	POLR2A	chr2:38976569-38979156	GM12892	blood:	n/a	n/a
9	TBL1XR1	chr2:38976613-38979296	K562	blood:	n/a	n/a
10	PML	chr2:38976814-38979147	GM12878	blood:	n/a	n/a
11	ELK1	chr2:38976639-38977051	K562	blood:	n/a	n/a
12	POLR2A	chr2:38976268-38979131	PFSK-1	brain:	n/a	n/a
13	WRNIP1	chr2:38976700-38977519	GM12878	blood:	n/a	n/a
14	GATA3	chr2:38976887-38979203	A549	lung:	n/a	chr2:38978735-38978746 chr2:38978927-38978934 chr2:38976996-38977007
15	POLR2A	chr2:38972076-38978836	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:38976610-38979278	SK-N-SH	brain:	n/a	n/a
17	USF2	chr2:38976867-38977557	K562	blood:	n/a	n/a
18	POLR2A	chr2:38976017-38979116	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:38973195-38979314	PANC-1	pancreas:	n/a	n/a
20	SIN3A	chr2:38976708-38979442	H1-hESC	embryonic stem cell:	n/a	chr2:38978586-38978597
21	HEY1	chr2:38976563-38978774	K562	blood:	n/a	n/a
22	POLR2A	chr2:38976768-38979496	PANC-1	pancreas:	n/a	n/a
23	NFATC1	chr2:38976918-38977659	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:38976575-38979505	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr2:38975842-38979011	GM12892	blood:	n/a	n/a
26	MXI1	chr2:38973236-38979955	SK-N-SH	brain:	n/a	chr2:38978665-38978680
27	POLR2A	chr2:38968189-38979081	GM12878	blood:	n/a	n/a
28	CEBPB	chr2:38976850-38977636	GM12878	blood:	n/a	n/a
29	TCF12	chr2:38976855-38979513	A549	lung:	n/a	n/a
30	CHD2	chr2:38976591-38978977	K562	blood:	n/a	chr2:38977797-38977807
31	POLR2A	chr2:38976080-38979142	K562	blood:	n/a	n/a
32	POLR2A	chr2:38967761-38979649	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr2:38968012-38979405	GM12891	blood:	n/a	n/a
34	RFX5	chr2:38976889-38977903	K562	blood:	n/a	n/a
35	CHD1	chr2:38976598-38979254	H1-hESC	embryonic stem cell:	n/a	chr2:38977797-38977807 chr2:38979174-38979184 chr2:38979181-38979191
36	POLR2A	chr2:38968110-38979132	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr2:38976552-38979445	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr2:38976909-38977068	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr2:38976575-38978825	A549	lung:	n/a	n/a
40	MYC	chr2:38976566-38979508	A549	lung:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
41	POLR2A	chr2:38976775-38977636	U87	brain:	n/a	n/a
42	RCOR1	chr2:38976883-38979063	K562	blood:	n/a	n/a
43	POLR2A	chr2:38976718-38978964	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr2:38976648-38979061	MCF10A-Er-Src	breast:	n/a	n/a
45	MXI1	chr2:38976601-38979588	IMR90	lung:	n/a	chr2:38978665-38978680
46	POLR2A	chr2:38976888-38979215	K562	blood:	n/a	n/a
47	POLR2A	chr2:38976691-38979045	HUVEC	blood vessel:	n/a	n/a
48	MXI1	chr2:38976546-38978889	K562	blood:	n/a	chr2:38978665-38978680
49	POLR2A	chr2:38976629-38978855	GM12891	blood:	n/a	n/a
50	POLR2A	chr2:38976577-38978894	Hela-S3	cervix:	n/a	n/a

No data

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38694392..38697195-chr2:38976226..38979289,3	K562	blood:
2	chr2:38976823..38979247-chr4:785282..787385,2	MCF-7	breast:
3	chr15:72409880..72410484-chr2:38976828..38977720,2	Hela-S3	cervix:
4	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
5	chr2:38976877..38979785-chr2:39100480..39105632,13	K562	blood:
6	chr2:38976218..38980921-chr2:39003670..39007764,15	K562	blood:
7	chr2:38975187..38978600-chr2:39347007..39351369,4	K562	blood:
8	chr19:5689960..5691696-chr2:38976849..38978490,2	K562	blood:
9	chr2:38976891..38979056-chr2:39028521..39033921,5	MCF-7	breast:
10	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
11	chr2:38762042..38765801-chr2:38976684..38979922,4	MCF-7	breast:
12	chr2:38976392..38979029-chr2:39027754..39033871,6	K562	blood:
13	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
14	chr2:38828577..38831705-chr2:38976861..38979916,6	MCF-7	breast:
15	chr2:38812622..38815204-chr2:38976239..38979096,3	K562	blood:
16	chr2:38891861..38895889-chr2:38976029..38979857,7	K562	blood:
17	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
18	chr2:38976661..38978798-chr2:39083252..39086476,5	MCF-7	breast:
19	chr2:38976457..38978515-chr2:39347011..39349138,2	K562	blood:
20	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
21	chr2:38975535..38978590-chr2:39035789..39038871,3	MCF-7	breast:
22	chr2:38602255..38605343-chr2:38976114..38979530,4	K562	blood:
23	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
24	chr2:38300805..38303904-chr2:38976182..38979449,4	MCF-7	breast:
25	chr2:38975156..38979928-chr2:39002986..39007194,11	MCF-7	breast:
26	chr2:38602430..38604455-chr2:38976753..38978503,3	K562	blood:
27	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
28	chr2:38976206..38978531-chr6:26156385..26159468,3	MCF-7	breast:
29	chr2:38976573..38978521-chr7:139025166..139027666,2	MCF-7	breast:
30	chr2:38975839..38978922-chr2:47400598..47403972,4	K562	blood:
31	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:

No data

Variant related genes	Relation type
SRSF7	TF binding region
GEMIN6	TF binding region
ENSG00000223922	Chromatin interaction
ENSG00000269955	Chromatin interaction
ENSG00000271443	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000138061	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000188010	Chromatin interaction
ENSG00000066933	Chromatin interaction
ENSG00000164898	Chromatin interaction
ENSG00000130255	Chromatin interaction
ENSG00000232114	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000115904	Chromatin interaction
ENSG00000231367	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000163214	Chromatin interaction
ENSG00000168993	Chromatin interaction
ENSG00000232973	Chromatin interaction
ENSG00000227238	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000119787	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs73930949	1.00[AMR][1000 genomes]
rs73930959	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv2763640	chr2:38954419-38977371	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
5	esv1834132	chr2:38955977-38977612	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	43 gene(s)	inside rSNPs	diseases
6	esv1836070	chr2:38955977-38977612	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38970000-38977400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
2	chr2:38972200-38977600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
3	chr2:38972400-38977600	Transcr. at gene 5' and 3'	A549	lung
4	chr2:38972600-38978400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:38972800-38977200	Weak transcription	Gastric	stomach
6	chr2:38973200-38978400	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr2:38973400-38978400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
8	chr2:38973600-38977200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:38973600-38977400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:38973800-38977200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
11	chr2:38973800-38978400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
12	chr2:38974200-38977400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:38974200-38977600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
14	chr2:38974600-38977600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
15	chr2:38974800-38977000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:38974800-38977400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
17	chr2:38974800-38977400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:38974800-38977600	Transcr. at gene 5' and 3'	NHEK	skin
19	chr2:38975000-38977400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
20	chr2:38975200-38977000	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
21	chr2:38975200-38977200	Transcr. at gene 5' and 3'	Hela-S3	cervix
22	chr2:38975400-38977200	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
23	chr2:38975400-38978400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
24	chr2:38975600-38977000	Weak transcription	Esophagus	oesophagus
25	chr2:38975600-38977400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
26	chr2:38975600-38977600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:38975600-38977600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
28	chr2:38975800-38977000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:38976000-38977000	Genic enhancers	Placenta	Placenta
30	chr2:38976000-38977200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
31	chr2:38976000-38977200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:38976000-38977200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:38976000-38977200	Transcr. at gene 5' and 3'	HSMM	muscle
34	chr2:38976000-38977200	Transcr. at gene 5' and 3'	NH-A	brain
35	chr2:38976000-38977400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:38976000-38977400	Transcr. at gene 5' and 3'	HepG2	liver
37	chr2:38976000-38977400	Transcr. at gene 5' and 3'	HMEC	breast
38	chr2:38976200-38977000	Transcr. at gene 5' and 3'	Liver	Liver
39	chr2:38976200-38977000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
40	chr2:38976200-38977000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
41	chr2:38976200-38977000	Transcr. at gene 5' and 3'	Thymus	Thymus
42	chr2:38976200-38977200	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
43	chr2:38976200-38977200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:38976200-38977200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
45	chr2:38976200-38977400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:38976200-38977400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
47	chr2:38976200-38977400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:38976200-38977400	Transcr. at gene 5' and 3'	NHLF	lung
49	chr2:38976200-38977400	Transcr. at gene 5' and 3'	Osteobl	bone
50	chr2:38976200-38979000	Active TSS	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links