Variant report

Variant	rs9288754
Chromosome Location	chr3:194825090-194825091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194819792..194821341-chr3:194822667..194825167,2	MCF-7	breast:
2	chr3:194750351..194753020-chr3:194825090..194827323,3	MCF-7	breast:
3	chr3:194590210..194593182-chr3:194824418..194827220,2	MCF-7	breast:
4	chr3:194822394..194825195-chr3:194825824..194828590,3	K562	blood:
5	chr3:194783220..194785678-chr3:194823694..194826162,2	K562	blood:
6	chr3:194818492..194820858-chr3:194824605..194827345,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10804419	1.00[CHB][hapmap]
rs1105819	0.85[CEU][hapmap]
rs13091190	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4079352	0.80[AMR][1000 genomes]
rs4677655	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677661	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4677803	1.00[CHB][hapmap]
rs903304	0.84[AMR][1000 genomes]
rs903306	0.85[CEU][hapmap];0.93[YRI][hapmap]
rs9825174	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs9860190	0.81[AMR][1000 genomes]
rs9867959	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879452	0.84[TSI][hapmap]

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	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
13	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9288754	RPL35A	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194802000-194826800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:194806800-194826400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:194808600-194827000	Weak transcription	Fetal Brain Female	brain
4	chr3:194814600-194827800	Enhancers	Fetal Heart	heart
5	chr3:194815200-194826800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:194815400-194827000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:194815800-194827000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:194815800-194830200	Weak transcription	Primary T cells from cord blood	blood
9	chr3:194816000-194826800	Weak transcription	Fetal Stomach	stomach
10	chr3:194816000-194830000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:194816400-194827000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:194816600-194826800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:194817200-194831200	Weak transcription	Gastric	stomach
14	chr3:194818200-194828800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:194818800-194826200	Weak transcription	Thymus	Thymus
16	chr3:194819000-194826800	Weak transcription	Dnd41	blood
17	chr3:194820800-194827600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:194821200-194826400	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:194821200-194827800	Enhancers	HUVEC	blood vessel
20	chr3:194821400-194825200	Enhancers	Osteobl	bone
21	chr3:194821400-194825400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:194821400-194825400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:194821600-194825200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:194822000-194827000	Weak transcription	Pancreas	Pancrea
25	chr3:194822000-194827000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:194822000-194846600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:194822200-194827000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr3:194822400-194825400	Enhancers	Primary B cells from cord blood	blood
29	chr3:194822400-194827000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:194822600-194827000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:194822600-194827000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:194823000-194825200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:194823000-194825200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr3:194823000-194826400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr3:194823000-194826400	Enhancers	A549	lung
36	chr3:194823200-194827800	Enhancers	Fetal Intestine Large	intestine
37	chr3:194823400-194827000	Enhancers	Placenta	Placenta
38	chr3:194823600-194826600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:194823600-194826800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:194823600-194827000	Weak transcription	GM12878-XiMat	blood
41	chr3:194823600-194831200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:194823800-194826800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:194823800-194826800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr3:194823800-194833200	Weak transcription	HSMM	muscle
45	chr3:194824000-194825200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:194824000-194825400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:194824000-194826800	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:194824000-194826800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:194824000-194827000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:194824000-194827000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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