Variant report

Variant	rs4741658
Chromosome Location	chr9:2241994-2241995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:2016060..2018467-chr9:2241276..2243249,2	K562	blood:
2	chr9:2231807..2233920-chr9:2241447..2243691,2	MCF-7	breast:
3	chr9:2240721..2243292-chr9:2621569..2623384,2	MCF-7	breast:
4	chr9:2229721..2232093-chr9:2241469..2243158,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236404	Chromatin interaction
ENSG00000080503	Chromatin interaction
ENSG00000147852	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10738622	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10965321	0.86[CHB][hapmap];0.90[GIH][hapmap]
rs10965323	0.91[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1408334	0.93[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv892057	chr9:2144687-2241994	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv892059	chr9:2198627-2255397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1033628	chr9:2215179-2303623	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv539927	chr9:2215179-2303623	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv892060	chr9:2218129-2261944	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv6457	chr9:2228493-2271756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv892061	chr9:2229694-2262889	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv1029947	chr9:2233969-2364269	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1015332	chr9:2235123-2361722	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv1022726	chr9:2235500-2361890	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv539928	chr9:2235500-2361890	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1033537	chr9:2235700-2361750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv539929	chr9:2235700-2361750	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv613127	chr9:2237390-2363874	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4741658	SMARCA2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2238000-2242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:2240400-2242400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:2241000-2242000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr9:2241000-2242000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:2241000-2242400	Active TSS	Brain Hippocampus Middle	brain
6	chr9:2241000-2242400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr9:2241000-2242800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr9:2241000-2242800	Active TSS	Brain Anterior Caudate	brain
9	chr9:2241000-2243200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:2241200-2242200	Enhancers	Spleen	Spleen
11	chr9:2241200-2242400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:2241200-2242600	Active TSS	Right Atrium	heart
13	chr9:2241200-2242800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr9:2241200-2242800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:2241200-2242800	Active TSS	Brain Angular Gyrus	brain
16	chr9:2241200-2242800	Flanking Active TSS	Fetal Muscle Leg	muscle
17	chr9:2241200-2242800	Flanking Active TSS	HUVEC	blood vessel
18	chr9:2241200-2243000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr9:2241200-2243000	Active TSS	Brain Germinal Matrix	brain
20	chr9:2241200-2243000	Active TSS	Fetal Kidney	kidney
21	chr9:2241200-2243200	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr9:2241400-2242000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:2241400-2242000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:2241400-2242000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:2241400-2242200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr9:2241400-2242200	Active TSS	Placenta Amnion	Placenta Amnion
27	chr9:2241400-2242200	Active TSS	NHLF	lung
28	chr9:2241400-2242200	Active TSS	Osteobl	bone
29	chr9:2241400-2242400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:2241400-2242400	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr9:2241400-2242400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:2241400-2242400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:2241400-2242600	Active TSS	Fetal Lung	lung
34	chr9:2241400-2242600	Active TSS	Ovary	ovary
35	chr9:2241400-2242800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:2241400-2242800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr9:2241400-2242800	Active TSS	Aorta	Aorta
38	chr9:2241400-2242800	Flanking Active TSS	Placenta	Placenta
39	chr9:2241400-2242800	Flanking Active TSS	Fetal Thymus	thymus
40	chr9:2241400-2242800	Active TSS	Psoas Muscle	Psoas
41	chr9:2241400-2243000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:2241400-2243000	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr9:2241400-2243000	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr9:2241400-2243000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:2241400-2243000	Flanking Active TSS	HMEC	breast
46	chr9:2241400-2243200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:2241400-2243200	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr9:2241400-2243600	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr9:2241600-2242000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr9:2241600-2242000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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