Variant report

Variant	rs6978810
Chromosome Location	chr7:21807211-21807212
allele	A/C
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:21295985..21296573-chr7:21806634..21807524,2	K562	blood:
2	chr7:21295823..21296612-chr7:21806734..21807628,5	MCF-7	breast:
3	chr7:21547043..21547991-chr7:21806813..21807569,3	MCF-7	breast:
4	chr7:21608001..21608689-chr7:21806668..21807749,3	MCF-7	breast:
5	chr7:21806980..21807646-chr7:22040800..22042221,5	MCF-7	breast:
6	chr7:21295299..21296544-chr7:21806799..21807582,4	MCF-7	breast:
7	chr7:21546916..21547496-chr7:21806696..21807577,2	MCF-7	breast:
8	chr7:21301191..21301804-chr7:21807075..21807617,2	MCF-7	breast:
9	chr7:21607583..21608493-chr7:21807066..21807743,2	MCF-7	breast:
10	chr7:21543389..21543978-chr7:21806643..21807254,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs17145331	0.91[CEU][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35428164	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4722053	0.91[CHB][hapmap]
rs6956997	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6977017	0.91[CHB][hapmap]
rs6978510	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6978811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1016063	chr7:21740433-21808410	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv470177	chr7:21801125-21817048	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6978810	SNX13	cis	cerebellum	SCAN
rs6978810	CIB1	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21796600-21810000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr7:21803400-21808000	Enhancers	Fetal Heart	heart
3	chr7:21804000-21808000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr7:21805200-21810000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:21805400-21810200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:21805400-21810600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr7:21805600-21809600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:21805600-21813800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr7:21805600-21813800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:21805800-21810800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:21806200-21812400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:21806800-21807600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr7:21806800-21807800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr7:21806800-21807800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr7:21807000-21810200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:21807200-21811600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

Quick Search:

Input of quick search could be:

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

what's new

Quick links