Variant report

Variant	rs3823861
Chromosome Location	chr7:120446128-120446129
allele	G/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:120444604..120449026-chr7:120452675..120456263,4	K562	blood:
2	chr7:120445873..120446554-chr7:120578030..120579156,3	MCF-7	breast:
3	chr7:120446018..120447563-chr7:120973530..120975197,2	K562	blood:
4	chr7:120440526..120443320-chr7:120444759..120447483,2	MCF-7	breast:
5	chr7:120445860..120446622-chr7:120721053..120722016,4	MCF-7	breast:
6	chr7:120445200..120446578-chr7:120497417..120498433,5	K562	blood:
7	chr7:120437232..120440783-chr7:120445669..120448518,3	K562	blood:
8	chr7:120445586..120446591-chr7:120580850..120581851,10	MCF-7	breast:
9	chr7:120445850..120446589-chr7:120497385..120498038,2	MCF-7	breast:
10	chr7:120439283..120443487-chr7:120444760..120448518,4	K562	blood:
11	chr7:120445313..120447921-chr7:120448553..120451279,2	K562	blood:
12	chr7:120446005..120446620-chr7:120580728..120581715,4	MCF-7	breast:
13	chr7:120445694..120446618-chr7:120580575..120581404,3	K562	blood:
14	chr7:120445663..120446844-chr7:120747170..120748613,7	K562	blood:
15	chr7:120446054..120446592-chr7:121187295..121188216,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000106025	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10225453	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10252911	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10266755	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10274689	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10279837	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11982493	0.85[ASN][1000 genomes]
rs12154976	0.91[CEU][hapmap]
rs12669167	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12673992	0.80[ASW][hapmap]
rs13231854	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17142976	0.82[CEU][hapmap]
rs17142995	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1859316	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1859319	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2097806	0.81[CHB][hapmap]
rs2107275	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107276	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2189974	0.91[CEU][hapmap]
rs2248890	0.81[JPT][hapmap]
rs2721341	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap]
rs2721343	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2721347	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2721354	0.86[JPT][hapmap]
rs3735467	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779386	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3779389	0.86[CHD][hapmap]
rs3823859	0.95[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41611	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41619	0.85[EUR][1000 genomes]
rs41620	0.85[EUR][1000 genomes]
rs41621	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41622	0.86[CEU][hapmap]
rs41623	0.95[CEU][hapmap]
rs41624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41627	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41628	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41629	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41631	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41632	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4445165	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730982	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs55855220	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6466759	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6466760	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6466761	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6466762	0.95[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6953454	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6958947	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6959328	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6961583	0.82[ASN][1000 genomes]
rs6964667	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6964786	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6971854	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6979247	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs714259	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs727228	0.81[CHB][hapmap]
rs73427866	0.86[ASN][1000 genomes]
rs7776721	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7781985	0.95[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7805211	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7805733	0.86[CEU][hapmap]
rs996903	0.80[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[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	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3823861	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120423000-120449200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:120425600-120470400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:120425800-120454400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:120427400-120466000	Weak transcription	Fetal Stomach	stomach
5	chr7:120430400-120468200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr7:120432600-120453800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr7:120432600-120455400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:120432600-120468400	Weak transcription	Lung	lung
9	chr7:120439200-120457800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:120439400-120469200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:120441200-120452600	Weak transcription	Fetal Intestine Small	intestine
12	chr7:120441400-120446400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:120442000-120449600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:120442600-120457400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr7:120443000-120488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:120443200-120446400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:120443400-120448600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:120443600-120446200	Weak transcription	HUVEC	blood vessel
19	chr7:120443800-120446200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:120444000-120457400	Weak transcription	Adipose Nuclei	Adipose
21	chr7:120444600-120446200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:120445200-120494400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr7:120445600-120447000	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr7:120445600-120447600	Enhancers	Fetal Heart	heart
25	chr7:120445600-120447800	Enhancers	Colon Smooth Muscle	Colon
26	chr7:120445800-120447800	Enhancers	Liver	Liver
27	chr7:120445800-120448600	Weak transcription	Fetal Intestine Large	intestine
28	chr7:120445800-120449400	Weak transcription	Fetal Muscle Leg	muscle
29	chr7:120446000-120446200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr7:120446000-120447400	Enhancers	Fetal Kidney	kidney
31	chr7:120446000-120476200	Weak transcription	Left Ventricle	heart

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