Variant report

Variant	rs2839850
Chromosome Location	chr7:107822198-107822199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr7:107822116-107822387	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr7:107822080-107822425	H1-hESC	embryonic stem cell:	n/a	n/a
3	HDAC2	chr7:107821966-107822397	H1-hESC	embryonic stem cell:	n/a	chr7:107822061-107822075 chr7:107822060-107822074 chr7:107822057-107822071
4	GTF2F1	chr7:107822002-107822446	H1-hESC	embryonic stem cell:	n/a	n/a
5	NANOG	chr7:107822113-107822387	H1-hESC	embryonic stem cell:	n/a	chr7:107822199-107822208
6	TCF12	chr7:107822067-107822388	H1-hESC	embryonic stem cell:	n/a	n/a
7	SP1	chr7:107821962-107822506	H1-hESC	embryonic stem cell:	n/a	n/a
8	POU5F1	chr7:107821983-107822504	H1-hESC	embryonic stem cell:	n/a	n/a
9	SRF	chr7:107822105-107822416	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr7:107821979-107822452	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF7	chr7:107822059-107822379	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr7:107821473-107822473	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr7:107821452-107822586	SK-N-SH	brain:	n/a	chr7:107821676-107821694 chr7:107821678-107821699
14	CHD2	chr7:107822019-107822407	H1-hESC	embryonic stem cell:	n/a	n/a
15	SRF	chr7:107822067-107822383	H1-hESC	embryonic stem cell:	n/a	n/a
16	SMC3	chr7:107821053-107822890	SK-N-SH	brain:	n/a	n/a
17	BCL11A	chr7:107822082-107822298	H1-hESC	embryonic stem cell:	n/a	n/a
18	EGR1	chr7:107822070-107822404	H1-hESC	embryonic stem cell:	n/a	n/a
19	SP1	chr7:107821930-107822501	H1-hESC	embryonic stem cell:	n/a	n/a
20	FOSL1	chr7:107822104-107822442	H1-hESC	embryonic stem cell:	n/a	n/a
21	POU5F1	chr7:107821999-107822365	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOSL1	chr7:107822084-107822484	H1-hESC	embryonic stem cell:	n/a	n/a
23	ZNF143	chr7:107822040-107822539	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr7:107822096-107822343	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr7:107820719-107823634	SK-N-SH	brain:	n/a	chr7:107821278-107821290
26	JUND	chr7:107821569-107822423	H1-hESC	embryonic stem cell:	n/a	n/a
27	TCF12	chr7:107822088-107822362	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr7:107820798-107822386	A549	lung:	n/a	chr7:107821676-107821694 chr7:107821678-107821699
29	RAD21	chr7:107821993-107822464	H1-hESC	embryonic stem cell:	n/a	n/a
30	NANOG	chr7:107821974-107822358	H1-hESC	embryonic stem cell:	n/a	chr7:107822199-107822208
31	TEAD4	chr7:107821958-107822480	H1-hESC	embryonic stem cell:	n/a	n/a
32	BCL11A	chr7:107821990-107822329	H1-hESC	embryonic stem cell:	n/a	n/a
33	ATF2	chr7:107821977-107822508	H1-hESC	embryonic stem cell:	n/a	n/a
34	EP300	chr7:107822068-107822436	H1-hESC	embryonic stem cell:	n/a	n/a
35	EGR1	chr7:107822096-107822411	H1-hESC	embryonic stem cell:	n/a	n/a
36	MXI1	chr7:107822159-107822217	Hela-S3	cervix:	n/a	n/a
37	JUND	chr7:107822150-107822383	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr7:107822057-107822325	H1-hESC	embryonic stem cell:	n/a	n/a
39	ATF2	chr7:107821935-107822435	H1-hESC	embryonic stem cell:	n/a	n/a
40	EP300	chr7:107822120-107822399	H1-hESC	embryonic stem cell:	n/a	n/a
41	TEAD4	chr7:107822083-107822420	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTBP2	chr7:107821948-107822433	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:107806656..107809513-chr7:107822092..107824990,2	MCF-7	breast:
2	chr7:107820337..107823179-chr7:108090688..108093464,2	MCF-7	breast:
3	chr7:107819867..107822378-chr7:107829973..107832574,2	K562	blood:
4	chr7:107817682..107823715-chr7:108094168..108099407,9	MCF-7	breast:
5	chr7:107821746..107823580-chr7:108165468..108166989,2	K562	blood:
6	chr7:107613209..107614826-chr7:107822149..107824634,2	K562	blood:
7	chr7:107821055..107823408-chr7:107926864..107929002,2	MCF-7	breast:

No data

Variant related genes	Relation type
NRCAM	TF binding region
ENSG00000135241	Chromatin interaction
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11767318	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs1735498	0.81[EUR][1000 genomes]
rs397656	0.81[EUR][1000 genomes]
rs399849	0.87[GIH][hapmap]
rs401573	0.83[GIH][hapmap]
rs448944	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs4730292	0.93[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv831089	chr7:107687618-107877240	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv888941	chr7:107796150-107863395	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1030222	chr7:107809927-107844916	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2839850	DOCK4	cis	parietal	SCAN
rs2839850	LAMB4	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107786800-107857800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:107787800-107844200	Weak transcription	Brain Germinal Matrix	brain
3	chr7:107791000-107824600	Weak transcription	HUVEC	blood vessel
4	chr7:107814200-107828400	Weak transcription	Fetal Intestine Small	intestine
5	chr7:107814800-107830400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:107815600-107829600	Weak transcription	Brain Substantia Nigra	brain
7	chr7:107817400-107828600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:107818200-107851800	Weak transcription	HSMMtube	muscle
9	chr7:107818600-107848400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:107818800-107826400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:107819200-107822200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr7:107819400-107822200	Weak transcription	Pancreas	Pancrea
13	chr7:107819800-107828400	Weak transcription	Brain Anterior Caudate	brain
14	chr7:107820000-107830000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr7:107820600-107867400	Weak transcription	Brain Angular Gyrus	brain
16	chr7:107820800-107824800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:107820800-107824800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr7:107820800-107827600	Weak transcription	Fetal Brain Female	brain
19	chr7:107820800-107830600	Weak transcription	Brain Hippocampus Middle	brain
20	chr7:107820800-107834600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:107820800-107840800	Weak transcription	Placenta	Placenta
22	chr7:107820800-107846800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:107820800-107850600	Weak transcription	Fetal Intestine Large	intestine
24	chr7:107820800-107851200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:107821000-107824400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:107821000-107824600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr7:107821000-107852200	Weak transcription	Fetal Muscle Leg	muscle
28	chr7:107821400-107822400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr7:107821400-107822800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:107821400-107823000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr7:107821400-107823400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr7:107821400-107823800	Genic enhancers	A549	lung
33	chr7:107821600-107850400	Weak transcription	Fetal Brain Male	brain
34	chr7:107821800-107822200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr7:107822000-107822200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr7:107822000-107822400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:107822000-107822400	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr7:107822000-107823400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:107822000-107834000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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