Variant report

Variant	rs10761346
Chromosome Location	chr9:97363620-97363621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97363454..97366255-chr9:97375188..97377706,2	K562	blood:
2	chr9:97363139..97364825-chr9:97366128..97368386,2	K562	blood:
3	chr9:97315606..97319704-chr9:97363491..97367544,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231806	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10114599	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115489	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1042144	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10761344	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821373	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821374	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10993275	0.82[CHB][hapmap]
rs16937175	0.82[CHB][hapmap]
rs1754435	0.83[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.80[YRI][hapmap]
rs1754439	0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs1977483	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1999122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1999123	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296708	0.82[CHB][hapmap]
rs2297084	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2772023	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993958	0.83[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.80[YRI][hapmap]
rs2993961	0.83[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap]
rs3824484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743960	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743961	0.82[CHB][hapmap]
rs4744359	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744362	0.82[CHB][hapmap]
rs548348	0.83[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs635108	0.82[ASN][1000 genomes]
rs6479555	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044434	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7856456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872412	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8192689	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs874248	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs9695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv466436	chr9:97343620-97369149	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv614917	chr9:97343620-97369149	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10761346	PHF2	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97347600-97374000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:97351800-97369200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:97356400-97365600	Weak transcription	Psoas Muscle	Psoas
4	chr9:97358000-97368800	Weak transcription	Gastric	stomach
5	chr9:97362000-97364400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr9:97362600-97364800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr9:97362600-97367000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:97362800-97364000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:97362800-97365600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:97363200-97364800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr9:97363200-97365400	Weak transcription	Stomach Mucosa	stomach
12	chr9:97363200-97365600	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:97363200-97365600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:97363400-97364000	Weak transcription	Fetal Intestine Small	intestine
15	chr9:97363400-97365600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:97363400-97366000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:97363600-97365000	Weak transcription	Liver	Liver
18	chr9:97363600-97365000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr9:97363600-97365000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:97363600-97365400	Weak transcription	Colonic Mucosa	Colon
21	chr9:97363600-97365400	Weak transcription	Fetal Intestine Large	intestine
22	chr9:97363600-97365400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:97363600-97365400	Weak transcription	HepG2	liver

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