Variant report

Variant	rs6775902
Chromosome Location	chr3:140995801-140995802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140994792..140996557-chr3:141006026..141007649,2	MCF-7	breast:
2	chr3:140994584..140997206-chr3:140998045..141000417,2	K562	blood:
3	chr3:140995281..140996903-chr3:140996967..140998531,2	MCF-7	breast:
4	chr3:140984792..140987604-chr3:140994461..140996447,2	K562	blood:

Variant related genes	Relation type
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11921252	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087169	0.82[ASW][hapmap];0.82[LWK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs16851272	0.83[MEX][hapmap]
rs1877223	0.83[MKK][hapmap]
rs3796259	0.82[CEU][hapmap]
rs4461396	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4683399	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6769909	0.82[CEU][hapmap]
rs6772725	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6772975	0.94[GIH][hapmap]
rs6786821	0.92[YRI][hapmap];0.84[AFR][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	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6775902	ACPL2	cis	parietal	SCAN
rs6775902	ACPL2	cis	cerebellum	SCAN
rs6775902	TRPC1	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
4	chr3:140978000-140998000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:140979000-141000800	Weak transcription	Fetal Kidney	kidney
6	chr3:140979000-141013200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:140980800-141005600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:140981000-140998400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:140981200-141013200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:140981200-141013400	Weak transcription	Colonic Mucosa	Colon
11	chr3:140981400-141001000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:140983600-141021600	Weak transcription	Esophagus	oesophagus
13	chr3:140984000-140997400	Weak transcription	Fetal Brain Female	brain
14	chr3:140984200-141000800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:140984600-140997600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:140984800-141006400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:140986200-140997600	Weak transcription	Brain Anterior Caudate	brain
18	chr3:140986200-140997600	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:140986200-140997600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:140986200-140998000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:140986200-141000800	Weak transcription	Fetal Lung	lung
22	chr3:140986800-140997400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:140987200-140997400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:140987800-140997600	Weak transcription	HSMMtube	muscle
25	chr3:140988200-141022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:140988400-141001800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:140990800-140998600	Weak transcription	Gastric	stomach
28	chr3:140991000-140996400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:140991000-140996800	Weak transcription	Fetal Intestine Large	intestine
30	chr3:140991000-140997400	Weak transcription	Right Atrium	heart
31	chr3:140991000-140997800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:140991000-140999600	Weak transcription	Pancreas	Pancrea
33	chr3:140991800-140996800	Enhancers	Placenta	Placenta
34	chr3:140992200-140997600	Weak transcription	Brain Angular Gyrus	brain
35	chr3:140993200-141014200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:140993400-140997200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:140993400-140998400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:140993600-140997600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:140993600-141004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:140993800-140996400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:140993800-140996800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:140993800-140997200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:140993800-140997400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:140993800-140997600	Weak transcription	Left Ventricle	heart
45	chr3:140993800-140998400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:140993800-140998600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:140993800-140999600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:140994000-140996200	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:140994000-140996400	Weak transcription	Fetal Heart	heart
50	chr3:140994000-140997000	Weak transcription	Spleen	Spleen

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