Variant report

Variant	rs12376117
Chromosome Location	chr9:6411838-6411839
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr9:6411777-6412070	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr9:6411824-6414615	NB4	blood:	n/a	chr9:6412718-6412727 chr9:6413671-6413681 chr9:6412905-6412915
3	POLR2A	chr9:6411810-6414105	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:6410972..6413613-chr9:6564070..6565701,2	MCF-7	breast:
2	chr9:6411580..6414419-chr9:6755713..6757647,2	K562	blood:
3	chr9:6411739..6415458-chr9:6420668..6426596,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf38-2	chr9:6411816-6411865	XLOC_007638
2	lnc-C9orf38-2	chr9:6411815-6411865	NONHSAT130128

Variant related genes	Relation type
UHRF2	TF binding region
ENSG00000178445	Chromatin interaction
ENSG00000147854	Chromatin interaction
ENSG00000107077	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10115362	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10124572	0.82[ASN][1000 genomes]
rs10733529	0.86[ASN][1000 genomes]
rs10739097	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10739098	0.87[ASN][1000 genomes]
rs10739099	0.86[ASN][1000 genomes]
rs10739100	0.86[ASN][1000 genomes]
rs10739102	0.83[ASN][1000 genomes]
rs10758783	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758784	0.85[ASN][1000 genomes]
rs10758785	0.86[ASN][1000 genomes]
rs10758786	0.85[ASN][1000 genomes]
rs10758787	0.85[ASN][1000 genomes]
rs10758788	0.86[ASN][1000 genomes]
rs10758789	0.85[ASN][1000 genomes]
rs10758790	0.85[ASN][1000 genomes]
rs10758792	0.85[ASN][1000 genomes]
rs10815411	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10815412	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10815428	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10975552	0.84[ASN][1000 genomes]
rs10975553	0.83[ASN][1000 genomes]
rs10975557	0.85[ASN][1000 genomes]
rs10975579	0.84[ASN][1000 genomes]
rs10975582	0.84[ASN][1000 genomes]
rs10975583	0.88[ASN][1000 genomes]
rs10975585	0.89[ASN][1000 genomes]
rs1156747	0.89[ASN][1000 genomes]
rs11790625	0.84[ASN][1000 genomes]
rs12346455	0.80[ASN][1000 genomes]
rs12351293	0.82[ASN][1000 genomes]
rs1322171	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13292799	0.80[ASN][1000 genomes]
rs1381035	0.84[ASN][1000 genomes]
rs1381036	0.84[ASN][1000 genomes]
rs1381037	0.83[ASN][1000 genomes]
rs1575263	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1575264	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16924434	0.83[ASN][1000 genomes]
rs16924562	0.82[ASN][1000 genomes]
rs16924591	0.81[ASN][1000 genomes]
rs1824537	0.83[ASN][1000 genomes]
rs1870696	0.80[ASN][1000 genomes]
rs1903419	0.84[ASN][1000 genomes]
rs2065074	0.83[ASN][1000 genomes]
rs2065075	0.86[ASN][1000 genomes]
rs2169282	0.84[ASN][1000 genomes]
rs2169283	0.85[ASN][1000 genomes]
rs2169286	0.89[ASN][1000 genomes]
rs2381444	0.84[ASN][1000 genomes]
rs4384035	0.83[ASN][1000 genomes]
rs4740844	0.86[ASN][1000 genomes]
rs4740845	0.86[ASN][1000 genomes]
rs4742181	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4742199	0.86[ASN][1000 genomes]
rs4742201	0.85[ASN][1000 genomes]
rs4742202	0.85[ASN][1000 genomes]
rs504698	0.81[ASN][1000 genomes]
rs55960819	0.82[ASN][1000 genomes]
rs56218473	0.87[ASN][1000 genomes]
rs56396114	0.82[ASN][1000 genomes]
rs56939673	0.86[ASN][1000 genomes]
rs569866	0.81[ASN][1000 genomes]
rs67852216	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7022186	0.84[ASN][1000 genomes]
rs7027302	0.82[ASN][1000 genomes]
rs7033940	0.82[ASN][1000 genomes]
rs7039175	0.82[EUR][1000 genomes]
rs719724	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs719725	0.87[ASN][1000 genomes]
rs73401679	0.82[ASN][1000 genomes]
rs7853059	0.82[ASN][1000 genomes]
rs7853834	0.82[ASN][1000 genomes]
rs7857628	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7860427	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7860966	0.82[ASN][1000 genomes]
rs7861073	0.82[ASN][1000 genomes]
rs7861559	0.82[ASN][1000 genomes]
rs7865955	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking 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	68 gene(s)	inside rSNPs	diseases
6	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv1023419	chr9:6393886-6415025	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6405400-6412200	Weak transcription	Thymus	Thymus
2	chr9:6408200-6412200	Weak transcription	Primary T cells from cord blood	blood
3	chr9:6408800-6412200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:6408800-6412400	Weak transcription	Pancreas	Pancrea
5	chr9:6409000-6412200	Weak transcription	NHEK	skin
6	chr9:6409800-6412400	Weak transcription	Liver	Liver
7	chr9:6410000-6412200	Enhancers	Primary B cells from peripheral blood	blood
8	chr9:6410000-6412400	Enhancers	Primary B cells from cord blood	blood
9	chr9:6410000-6412600	Enhancers	Primary hematopoietic stem cells	blood
10	chr9:6410600-6412000	Weak transcription	Fetal Stomach	stomach
11	chr9:6410600-6412200	Weak transcription	Brain Angular Gyrus	brain
12	chr9:6410600-6412400	Enhancers	GM12878-XiMat	blood
13	chr9:6410800-6412200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:6410800-6412200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:6411000-6412200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:6411000-6412200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr9:6411800-6412200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr9:6411800-6412200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr9:6411800-6412200	ZNF genes & repeats	Fetal Intestine Large	intestine
20	chr9:6411800-6412200	Enhancers	Fetal Thymus	thymus
21	chr9:6411800-6412400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:6411800-6412400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:6411800-6414200	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr9:6411800-6414800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr9:6411800-6415200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:6411800-6415600	Active TSS	ES-I3 Cell Line	embryonic stem cell

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