Variant report

Variant	rs10228542
Chromosome Location	chr7:128092238-128092239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:128092224-128092274	HCM	heart:	n/a
2	chr7:128092224-128092274	PANC-1	pancreas:	n/a
3	chr7:128092224-128092274	H1-hESC	embryonic stem cell:	embryo
4	chr7:128092224-128092274	NHBE	bronchial:	n/a
5	chr7:128092224-128092274	U87	brain:	n/a
6	chr7:128092224-128092274	GM12892	blood:	n/a
7	chr7:128092224-128092274	HMEC	breast:	n/a
8	chr7:128092224-128092274	SAEC	small airway:	n/a
9	chr7:128092224-128092274	CMK	blood:	n/a
10	chr7:128092224-128092274	HepG2	liver:	n/a
11	chr7:128092224-128092274	AoSMC	blood vessel:	n/a
12	chr7:128092224-128092274	AG09309	skin:	n/a
13	chr7:128092224-128092274	SK-N-SH_RA	brain:	n/a
14	chr7:128092224-128092274	GM19239	blood:	n/a
15	chr7:128092224-128092274	ECC-1	luminal epithelium:	n/a
16	chr7:128092224-128092274	MCF10A-Er-Src	breast:	n/a
17	chr7:128092224-128092274	NB4	blood:	n/a
18	chr7:128092224-128092274	AG09319	gingival:	n/a
19	chr7:128092224-128092274	A549	lung:	n/a
20	chr7:128092224-128092274	HEK293	kidney:	embryo
21	chr7:128092224-128092274	Jurkat	blood:	n/a
22	chr7:128092224-128092274	HRPEpiC	eye:	n/a
23	chr7:128092224-128092274	ProgFib	skin:	n/a
24	chr7:128092224-128092274	RPTEC	kidney:	n/a
25	chr7:128092224-128092274	HRCEpiC	kidney:	n/a
26	chr7:128092224-128092274	HPAEpiC	pulmonary alveolar:	n/a
27	chr7:128092224-128092274	ovcar-3	ovarian:	n/a
28	chr7:128092224-128092274	SK-N-MC	brain:	n/a
29	chr7:128092224-128092274	MCF-7	breast:	n/a
30	chr7:128092224-128092274	HCPEpiC	choroid plexus:	n/a
31	chr7:128092224-128092274	Hela-S3	cervix:	n/a
32	chr7:128092224-128092274	HCT-116	colon:	n/a
33	chr7:128092224-128092274	HL-60	blood:	n/a
34	chr7:128092224-128092274	GM12891	blood:	n/a
35	chr7:128092224-128092274	PFSK-1	brain:	n/a
36	chr7:128092224-128092274	Hepatocyte	liver:	n/a
37	chr7:128092224-128092274	HAEpiC	amniotic membrane:	n/a
38	chr7:128092224-128092274	AG04449	skin:	fetal
39	chr7:128092224-128092274	NT2-D1	testis:	n/a
40	chr7:128092224-128092274	HUVEC	blood vessel:	n/a
41	chr7:128092224-128092274	SK-N-SH	brain:	n/a
42	chr7:128092224-128092274	Caco-2	colon:	n/a
43	chr7:128092224-128092274	HRE	kidney:	n/a
44	chr7:128092224-128092274	HEEpiC	esophagus:	n/a
45	chr7:128092224-128092274	BJ	skin:	n/a
46	chr7:128092224-128092274	GM06990	blood:	n/a
47	chr7:128092224-128092274	PrEC	prostate:	n/a
48	chr7:128092224-128092274	HCF	heart:	n/a
49	chr7:128092224-128092274	AG04450	lung:	fetal
50	chr7:128092224-128092274	T-47D	breast:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:128077598..128080477-chr7:128092228..128095663,3	K562	blood:
2	chr7:128072011..128074476-chr7:128091797..128093938,2	K562	blood:
3	chr7:128090610..128092505-chr7:128094559..128097059,2	MCF-7	breast:
4	chr7:128082541..128090035-chr7:128090151..128101015,22	MCF-7	breast:
5	chr7:128090220..128093151-chr7:128093221..128095086,2	K562	blood:
6	chr7:128081326..128084336-chr7:128089297..128092951,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000240758	CpG island
ENSG00000273184	CpG island
HILPDA	CpG island
ENSG00000240758	Chromatin interaction
ENSG00000273184	Chromatin interaction
ENSG00000228700	Chromatin interaction
ENSG00000238590	Chromatin interaction
ENSG00000135245	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10239919	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10247945	0.81[EUR][1000 genomes]
rs11562031	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12111997	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12113427	0.83[EUR][1000 genomes]
rs1560215	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17152065	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28391244	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28429588	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3802003	0.80[MEX][hapmap]
rs4731449	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs57075087	0.87[EUR][1000 genomes]
rs6944392	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap]
rs6978246	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72624928	0.85[EUR][1000 genomes]
rs732831	0.83[YRI][hapmap]
rs7779455	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7779818	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7779945	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7781310	0.81[EUR][1000 genomes]
rs7783540	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7784120	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7784564	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7806193	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv608401	chr7:128083454-128108776	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10228542	ARF5	cis	parietal	SCAN
rs10228542	CCDC136	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128075600-128093800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:128075600-128093800	Weak transcription	Pancreas	Pancrea
3	chr7:128078600-128095200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:128084600-128095800	Weak transcription	Gastric	stomach
5	chr7:128084800-128093600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:128084800-128093800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:128086400-128095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:128086600-128093800	Weak transcription	Right Atrium	heart
9	chr7:128086800-128093800	Weak transcription	Brain Anterior Caudate	brain
10	chr7:128086800-128093800	Weak transcription	Right Ventricle	heart
11	chr7:128087000-128092400	Weak transcription	K562	blood
12	chr7:128087000-128093400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr7:128087000-128093600	Weak transcription	Brain Hippocampus Middle	brain
14	chr7:128089000-128093800	Weak transcription	Stomach Mucosa	stomach
15	chr7:128090600-128093800	Weak transcription	HSMM	muscle
16	chr7:128090800-128093600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr7:128090800-128093600	Weak transcription	HSMMtube	muscle
18	chr7:128090800-128094000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:128090800-128094800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr7:128091000-128093400	Weak transcription	Left Ventricle	heart
21	chr7:128091000-128093600	Weak transcription	Fetal Heart	heart
22	chr7:128091000-128094000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:128091000-128095000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr7:128091200-128093400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr7:128091200-128093600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:128091800-128092400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr7:128091800-128092400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:128091800-128093000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:128091800-128094400	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr7:128091800-128094800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr7:128092000-128092400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr7:128092000-128092600	Enhancers	A549	lung
33	chr7:128092200-128092400	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr7:128092200-128092600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr7:128092200-128092600	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr7:128092200-128093200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:128092200-128093200	Weak transcription	GM12878-XiMat	blood
38	chr7:128092200-128094600	Enhancers	Fetal Intestine Large	intestine
39	chr7:128092200-128095200	Enhancers	HepG2	liver

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