Variant report

Variant	rs1468141
Chromosome Location	chr7:104004570-104004571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10254423	0.81[ASN][1000 genomes]
rs10953426	0.86[YRI][hapmap]
rs1465197	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2188491	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2385234	0.85[ASN][1000 genomes]
rs4729996	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs4729999	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4730000	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6465983	0.86[YRI][hapmap]
rs7787976	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs7787988	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs7788386	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs7794488	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7800144	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv608067	chr7:103944237-104029408	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1468141	ZNHIT1	cis	parietal	SCAN
rs1468141	CDHR3	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104001600-104005200	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr7:104002400-104005200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr7:104002800-104005200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr7:104002800-104005400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr7:104003000-104005000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr7:104003000-104005000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:104003200-104004600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:104003200-104004800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:104003200-104005200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr7:104003600-104005200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr7:104003800-104004800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr7:104003800-104005400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:104004000-104004600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:104004000-104005000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr7:104004000-104005600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr7:104004200-104008400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:104004200-104010600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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