Variant report

Variant	rs10758784
Chromosome Location	chr9:6415025-6415026
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:6413231..6415998-chr9:6419721..6423966,4	MCF-7	breast:
2	chr9:6411739..6415458-chr9:6420668..6426596,8	K562	blood:
3	chr9:6412168..6415418-chr9:6418500..6425043,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10115362	0.86[ASN][1000 genomes]
rs10115883	0.94[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap]
rs10122116	0.89[JPT][hapmap]
rs10124572	0.84[ASN][1000 genomes]
rs10733529	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739098	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739099	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10739100	0.94[ASN][1000 genomes]
rs10739102	0.91[ASN][1000 genomes]
rs10758783	0.86[ASN][1000 genomes]
rs10758785	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10758786	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758787	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758788	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10758789	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758790	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758791	0.85[ASN][1000 genomes]
rs10758792	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10815428	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10815432	0.87[AFR][1000 genomes]
rs10815435	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10975579	0.95[ASN][1000 genomes]
rs10975582	0.94[ASN][1000 genomes]
rs10975583	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10975585	0.90[ASN][1000 genomes]
rs10975595	0.88[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10975605	0.94[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap]
rs1156747	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.91[ASN][1000 genomes]
rs11790625	0.85[ASN][1000 genomes]
rs11791651	0.83[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs11795355	0.84[JPT][hapmap]
rs12346455	0.82[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12347573	0.88[CEU][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12351293	0.84[ASN][1000 genomes]
rs12376117	0.85[ASN][1000 genomes]
rs13283381	0.88[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs13289925	0.89[EUR][1000 genomes]
rs13291472	0.94[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13292799	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13296970	0.83[EUR][1000 genomes]
rs13298500	0.80[CHB][hapmap];0.94[CHD][hapmap];0.84[TSI][hapmap]
rs13301146	0.83[EUR][1000 genomes]
rs13440427	0.80[ASN][1000 genomes]
rs1381035	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1381036	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1381037	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16924328	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs16924562	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs16924591	0.82[ASN][1000 genomes]
rs16924624	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs16924626	0.89[JPT][hapmap]
rs16924631	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap]
rs16924634	0.88[CHD][hapmap]
rs1824537	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1870696	0.82[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1903419	1.00[ASW][hapmap];0.88[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2065074	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2065075	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2169283	0.94[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs2169286	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2381444	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs33962342	0.82[CHD][hapmap]
rs3739654	0.82[ASW][hapmap];0.94[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs380674	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs414107	0.82[ASN][1000 genomes]
rs4384035	0.85[ASN][1000 genomes]
rs452135	0.82[ASN][1000 genomes]
rs4556138	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4740844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4740845	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742199	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742201	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742202	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742204	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs504698	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs530722	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55960819	0.84[ASN][1000 genomes]
rs56218473	0.89[ASN][1000 genomes]
rs56396114	0.84[ASN][1000 genomes]
rs56939673	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs569866	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6477086	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6477087	0.88[CEU][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67852216	0.85[ASN][1000 genomes]
rs7027302	0.84[ASN][1000 genomes]
rs7029772	0.81[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs7033940	0.83[ASN][1000 genomes]
rs73401679	0.83[ASN][1000 genomes]
rs7848831	0.86[EUR][1000 genomes]
rs7852539	1.00[CEU][hapmap];0.84[JPT][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7853059	0.83[ASN][1000 genomes]
rs7853834	0.83[ASN][1000 genomes]
rs7857628	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7860427	0.85[ASN][1000 genomes]
rs7860966	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7861073	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7861559	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7865955	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs7871134	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7873756	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
13	esv3440128	chr9:6412477-6415325	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10758784	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6411800-6415200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:6411800-6415600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr9:6412200-6415200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:6412200-6415200	Active TSS	Aorta	Aorta
5	chr9:6412200-6415200	Active TSS	Right Atrium	heart
6	chr9:6412200-6415400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr9:6412200-6415400	Active TSS	Fetal Intestine Large	intestine
8	chr9:6412200-6415400	Active TSS	Ovary	ovary
9	chr9:6412200-6415400	Active TSS	Psoas Muscle	Psoas
10	chr9:6412200-6415800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:6412400-6415200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:6412400-6415200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr9:6412400-6415200	Active TSS	Right Ventricle	heart
14	chr9:6412400-6415200	Active TSS	A549	lung
15	chr9:6412400-6415200	Active TSS	Hela-S3	cervix
16	chr9:6412400-6415400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr9:6412400-6415400	Active TSS	HSMMtube	muscle
18	chr9:6412600-6415200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:6412600-6415200	Active TSS	Fetal Intestine Small	intestine
20	chr9:6412600-6415200	Active TSS	Stomach Smooth Muscle	stomach
21	chr9:6412600-6415200	Active TSS	NHDF-Ad	bronchial
22	chr9:6412600-6415400	Active TSS	NHLF	lung
23	chr9:6412800-6415200	Active TSS	NHEK	skin
24	chr9:6412800-6415400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:6412800-6415400	Active TSS	Muscle Satellite Cultured Cells	--
26	chr9:6412800-6415400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:6412800-6415800	Active TSS	HMEC	breast
28	chr9:6413000-6415200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:6413000-6415200	Active TSS	Primary T cells fromperipheralblood	blood
30	chr9:6413000-6415200	Active TSS	Fetal Thymus	thymus
31	chr9:6413000-6415200	Active TSS	Thymus	Thymus
32	chr9:6413000-6415200	Active TSS	HUVEC	blood vessel
33	chr9:6413000-6415200	Active TSS	K562	blood
34	chr9:6413000-6415200	Active TSS	NH-A	brain
35	chr9:6413400-6415600	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr9:6413600-6415600	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr9:6413800-6415200	Active TSS	HepG2	liver
38	chr9:6414000-6415400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr9:6414000-6415400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:6414000-6415600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr9:6414200-6415200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:6414200-6415200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr9:6414200-6415200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr9:6414200-6415200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:6414200-6415600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:6414200-6415600	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr9:6414200-6415800	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr9:6414200-6415800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr9:6414200-6415800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:6414200-6416000	Transcr. at gene 5' and 3'	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links