Variant report

Variant	rs4742741
Chromosome Location	chr9:101539601-101539602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101539424..101541523-chr9:101551442..101554198,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10121153	0.92[ASN][1000 genomes]
rs1022796	0.93[ASN][1000 genomes]
rs10739690	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10760475	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10760479	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10760494	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10819266	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10819308	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs10819320	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs10987749	0.90[ASN][1000 genomes]
rs11791440	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12057064	0.86[EUR][1000 genomes]
rs1555519	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]
rs168083	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs337569	0.82[TSI][hapmap]
rs337581	0.82[EUR][1000 genomes]
rs337591	0.85[TSI][hapmap]
rs3933477	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs420158	0.85[TSI][hapmap]
rs422531	0.84[EUR][1000 genomes]
rs4742737	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4742738	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4742745	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743278	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4743281	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4743282	0.88[ASN][1000 genomes]
rs580809	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs60698775	0.84[EUR][1000 genomes]
rs6478839	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478845	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7018907	0.96[ASN][1000 genomes]
rs7020056	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7027405	0.95[ASN][1000 genomes]
rs7027771	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]
rs7028766	0.87[EUR][1000 genomes]
rs7035107	0.85[TSI][hapmap]
rs7035722	0.87[EUR][1000 genomes]
rs7038640	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]
rs7047722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs72735324	0.84[EUR][1000 genomes]
rs72735326	0.87[EUR][1000 genomes]
rs7357783	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7469116	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7853904	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7861186	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs7865233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886821	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9919074	0.84[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4742741	ANKS6	Cis_1M	lymphoblastoid	RTeQTL
rs4742741	C9orf130	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101494400-101553000	Weak transcription	Fetal Heart	heart
2	chr9:101496600-101549400	Weak transcription	Small Intestine	intestine
3	chr9:101506800-101553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:101508600-101557400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:101514400-101553400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:101518800-101557200	Weak transcription	Psoas Muscle	Psoas
7	chr9:101521200-101557600	Weak transcription	Fetal Brain Male	brain
8	chr9:101523600-101542600	Weak transcription	Stomach Mucosa	stomach
9	chr9:101526400-101549400	Strong transcription	Stomach Smooth Muscle	stomach
10	chr9:101528200-101543800	Weak transcription	HMEC	breast
11	chr9:101530200-101547600	Weak transcription	NHDF-Ad	bronchial
12	chr9:101530400-101557800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:101531400-101540400	Strong transcription	K562	blood
14	chr9:101532400-101540600	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr9:101533800-101553200	Strong transcription	Fetal Stomach	stomach
16	chr9:101534000-101557600	Weak transcription	Right Atrium	heart
17	chr9:101534200-101542200	Weak transcription	Fetal Thymus	thymus
18	chr9:101534400-101545800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr9:101535600-101553400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr9:101535800-101541200	Weak transcription	Fetal Kidney	kidney
21	chr9:101535800-101542200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:101535800-101552000	Weak transcription	Thymus	Thymus
23	chr9:101535800-101553400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:101535800-101557400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:101536000-101541200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:101536000-101543600	Weak transcription	NHEK	skin
27	chr9:101536000-101544400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:101536000-101553200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:101536000-101557600	Weak transcription	Primary B cells from cord blood	blood
30	chr9:101536200-101543400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:101536200-101543600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:101536200-101543600	Weak transcription	Osteobl	bone
33	chr9:101536200-101543800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:101536200-101544400	Weak transcription	HSMM	muscle
35	chr9:101536200-101553400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr9:101536400-101541000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:101536400-101543600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:101536400-101543800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:101536600-101543800	Weak transcription	Liver	Liver
40	chr9:101536600-101544400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr9:101536600-101557600	Weak transcription	Brain Germinal Matrix	brain
42	chr9:101536800-101540200	Weak transcription	Esophagus	oesophagus
43	chr9:101536800-101540800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:101536800-101541000	Weak transcription	Lung	lung
45	chr9:101536800-101542600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr9:101536800-101543200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr9:101536800-101543400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:101536800-101543600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr9:101536800-101543600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr9:101536800-101543600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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