Variant report

Variant	rs7555638
Chromosome Location	chr1:247371918-247371919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247366973..247371599-chr1:247371697..247375755,6	MCF-7	breast:
2	chr1:247370160..247372066-chr1:247376870..247379073,2	MCF-7	breast:
3	chr1:247338400..247340247-chr1:247370932..247373277,2	K562	blood:
4	chr1:247371399..247373319-chr1:247494315..247496686,3	K562	blood:
5	chr1:247371907..247375145-chr1:247492885..247497524,4	MCF-7	breast:
6	chr1:247361273..247363730-chr1:247370221..247373518,3	K562	blood:
7	chr1:247249370..247251195-chr1:247370860..247372541,2	K562	blood:
8	chr1:247274493..247276812-chr1:247371838..247375899,3	K562	blood:
9	chr1:247371506..247373896-chr1:247494793..247496492,2	K562	blood:
10	chr1:247371861..247375582-chr1:247493463..247496360,5	MCF-7	breast:
11	chr1:247370277..247372519-chr1:247432525..247434040,2	K562	blood:
12	chr1:247370419..247372444-chr1:247470264..247472870,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NLRP3-4	chr1:247371783-247372435	NONHSAT010763

No data

Variant related genes	Relation type
ENSG00000162714	Chromatin interaction
ENSG00000252516	Chromatin interaction
ENSG00000221953	Chromatin interaction
ENSG00000227671	Chromatin interaction
ENSG00000224014	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11588486	0.93[ASN][1000 genomes]
rs12118988	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs12136392	0.91[ASN][1000 genomes]
rs12141741	0.86[CHB][hapmap];0.93[ASN][1000 genomes]
rs12141744	0.93[ASN][1000 genomes]
rs12145632	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs12732373	0.88[ASN][1000 genomes]
rs34660548	0.88[ASN][1000 genomes]
rs6700968	0.82[ASW][hapmap];0.93[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
6	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
8	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
10	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7555638	ZNF124	cis	cerebellum	SCAN
rs7555638	ZNF124	cis	parietal	SCAN
rs7555638	CNST	cis	parietal	SCAN
rs7555638	C1orf150	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247351800-247372400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr1:247353400-247372000	ZNF genes & repeats	GM12878-XiMat	blood
3	chr1:247354800-247372400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:247354800-247372400	Weak transcription	Right Ventricle	heart
5	chr1:247356000-247372400	Weak transcription	Brain Anterior Caudate	brain
6	chr1:247356000-247372400	Weak transcription	Fetal Brain Male	brain
7	chr1:247356000-247372600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:247356000-247372600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:247356200-247372400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:247356200-247372400	Weak transcription	Colonic Mucosa	Colon
11	chr1:247356400-247372400	Weak transcription	Gastric	stomach
12	chr1:247358400-247372400	Weak transcription	Fetal Heart	heart
13	chr1:247359000-247372600	Weak transcription	Fetal Kidney	kidney
14	chr1:247360600-247372400	Weak transcription	Fetal Lung	lung
15	chr1:247360600-247372400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:247362400-247373400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:247362600-247372400	Weak transcription	Psoas Muscle	Psoas
18	chr1:247362600-247372800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:247362800-247372400	Weak transcription	Pancreas	Pancrea
20	chr1:247363000-247372400	Weak transcription	Ovary	ovary
21	chr1:247363000-247372400	Weak transcription	NH-A	brain
22	chr1:247363200-247372600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:247363400-247372400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:247363400-247372400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:247363600-247372200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:247363600-247372400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:247363600-247372400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:247363600-247372400	Weak transcription	Placenta	Placenta
29	chr1:247363600-247372400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:247363600-247372400	Weak transcription	Osteobl	bone
31	chr1:247363600-247372600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:247363600-247372800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:247364000-247372600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:247364400-247372400	Weak transcription	NHDF-Ad	bronchial
35	chr1:247365600-247372800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:247365800-247372400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:247365800-247372400	Weak transcription	Esophagus	oesophagus
38	chr1:247366200-247372400	Weak transcription	Aorta	Aorta
39	chr1:247367000-247372400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:247367000-247372600	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr1:247367200-247372000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:247367600-247372400	Weak transcription	Fetal Intestine Large	intestine
43	chr1:247367800-247372400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:247367800-247372400	Weak transcription	HSMM	muscle
45	chr1:247368000-247372400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:247368000-247372400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:247368000-247372600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:247368200-247372000	Weak transcription	HUVEC	blood vessel
49	chr1:247368600-247372400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:247369000-247372800	ZNF genes & repeats	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links