Variant report

Variant	rs7038640
Chromosome Location	chr9:101553014-101553015
allele	G/T
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	RAD21	chr9:101552817-101554067	SK-N-SH	brain:	n/a	chr9:101553799-101553809 chr9:101553620-101553634 chr9:101553623-101553632 chr9:101553797-101553810 chr9:101553618-101553632 chr9:101553798-101553807 chr9:101553617-101553630 chr9:101553614-101553633 chr9:101553618-101553628 chr9:101553799-101553811 chr9:101553616-101553628 chr9:101553794-101553813
2	GATA2	chr9:101552809-101553167	SH-SY5Y	brain:	n/a	n/a
3	HEY1	chr9:101551978-101553020	K562	blood:	n/a	n/a
4	CTCF	chr9:101552790-101554029	SK-N-SH	brain:	n/a	chr9:101553618-101553631 chr9:101553795-101553816 chr9:101553611-101553632 chr9:101553793-101553811 chr9:101553616-101553634 chr9:101553798-101553808 chr9:101553623-101553631 chr9:101553794-101553810 chr9:101553796-101553809 chr9:101553621-101553634
5	CTCF	chr9:101552940-101554153	A549	lung:	n/a	chr9:101553618-101553631 chr9:101553795-101553816 chr9:101553611-101553632 chr9:101553793-101553811 chr9:101553616-101553634 chr9:101553798-101553808 chr9:101553623-101553631 chr9:101553794-101553810 chr9:101553796-101553809 chr9:101554042-101554055 chr9:101553621-101553634
6	SMC3	chr9:101552732-101554145	SK-N-SH	brain:	n/a	chr9:101553795-101553809 chr9:101553618-101553632
7	RCOR1	chr9:101552691-101553891	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:101552233..101554875-chr9:101569362..101571456,2	K562	blood:
2	chr9:101545059..101549166-chr9:101549298..101553118,4	MCF-7	breast:
3	chr9:101545621..101549470-chr9:101551390..101554188,5	MCF-7	breast:
4	chr9:101539424..101541523-chr9:101551442..101554198,3	MCF-7	breast:
5	chr9:101550225..101553756-chr9:101569289..101571539,3	MCF-7	breast:
6	chr9:101551293..101553847-chr9:101568036..101571328,4	K562	blood:
7	chr9:101550194..101555244-chr9:101566657..101571786,8	MCF-7	breast:

Variant related genes	Relation type
ANKS6	TF binding region
ENSG00000119514	Chromatin interaction
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10121153	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1022796	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739690	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10760475	0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10760479	0.82[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10760494	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819266	0.81[ASN][1000 genomes]
rs10819308	0.91[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10819320	0.91[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10987747	0.80[ASW][hapmap];0.87[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs10987749	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10987771	0.83[EUR][1000 genomes]
rs11791440	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12056975	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs1543506	0.87[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1555519	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2146255	0.83[EUR][1000 genomes]
rs33998698	0.83[EUR][1000 genomes]
rs3933477	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742737	0.86[ASN][1000 genomes]
rs4742738	0.82[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4742741	0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4742745	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743278	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743281	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743282	0.85[ASN][1000 genomes]
rs6478839	0.84[ASN][1000 genomes]
rs6478845	0.83[ASN][1000 genomes]
rs7018907	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7020056	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027405	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027771	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7047722	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7357783	0.85[ASN][1000 genomes]
rs7469116	0.88[ASN][1000 genomes]
rs7853904	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7861186	0.91[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7865233	0.85[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.90[ASN][1000 genomes]
rs9886821	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking 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	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7038640	C9orf130	cis	cerebellum	SCAN
rs7038640	ANKS6	Cis_1M	lymphoblastoid	RTeQTL
rs7038640	ZNF189	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101506800-101553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr9:101508600-101557400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr9:101514400-101553400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:101518800-101557200	Weak transcription	Psoas Muscle	Psoas
5	chr9:101521200-101557600	Weak transcription	Fetal Brain Male	brain
6	chr9:101530400-101557800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:101533800-101553200	Strong transcription	Fetal Stomach	stomach
8	chr9:101534000-101557600	Weak transcription	Right Atrium	heart
9	chr9:101535600-101553400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr9:101535800-101553400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr9:101535800-101557400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr9:101536000-101553200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:101536000-101557600	Weak transcription	Primary B cells from cord blood	blood
14	chr9:101536200-101553400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:101536600-101557600	Weak transcription	Brain Germinal Matrix	brain
16	chr9:101537000-101557400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:101542000-101553200	Weak transcription	HUVEC	blood vessel
18	chr9:101542600-101553200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:101544200-101557600	Weak transcription	Colonic Mucosa	Colon
20	chr9:101544800-101557600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr9:101545200-101557200	Weak transcription	Liver	Liver
22	chr9:101545400-101553200	Weak transcription	Brain Substantia Nigra	brain
23	chr9:101546200-101557600	Weak transcription	Left Ventricle	heart
24	chr9:101546400-101557200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr9:101546600-101553200	Weak transcription	Placenta	Placenta
26	chr9:101547000-101553400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:101547000-101557000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:101547400-101553600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:101547800-101553200	Strong transcription	Primary T cells from cord blood	blood
30	chr9:101549000-101553200	Strong transcription	K562	blood
31	chr9:101549600-101553200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:101549800-101553200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr9:101550000-101553200	Strong transcription	Fetal Intestine Small	intestine
34	chr9:101550200-101553200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr9:101550600-101557000	Weak transcription	Dnd41	blood
36	chr9:101551000-101553200	Weak transcription	GM12878-XiMat	blood
37	chr9:101551000-101557400	Weak transcription	Fetal Brain Female	brain
38	chr9:101551600-101553200	Strong transcription	HepG2	liver
39	chr9:101552000-101553200	Strong transcription	Thymus	Thymus
40	chr9:101552200-101553200	Weak transcription	Colon Smooth Muscle	Colon
41	chr9:101552400-101553200	Weak transcription	Fetal Kidney	kidney
42	chr9:101552400-101553200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr9:101552400-101553200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr9:101552400-101553400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:101552400-101553400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr9:101552400-101553400	Genic enhancers	HSMM	muscle
47	chr9:101552400-101554000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:101552400-101556800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:101552400-101557000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr9:101552400-101557400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links