Variant report

Variant	rs7636810
Chromosome Location	chr3:23967444-23967445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23966887..23969237-chr3:23985235..23987647,2	MCF-7	breast:
2	chr3:23967304..23969953-chr3:24001242..24004073,2	K562	blood:
3	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
4	chr3:23967043..23969562-chr3:24002136..24003656,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174738	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10865791	0.91[JPT][hapmap]
rs11129130	0.91[JPT][hapmap]
rs11717862	0.90[ASN][1000 genomes]
rs12631785	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs13091509	0.98[ASN][1000 genomes]
rs13095392	0.91[CHB][hapmap]
rs4078155	0.91[JPT][hapmap]
rs4241515	0.94[ASN][1000 genomes]
rs4241517	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4241520	0.91[ASN][1000 genomes]
rs4292186	0.91[JPT][hapmap]
rs4293661	0.91[JPT][hapmap]
rs4321479	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs4578971	0.91[JPT][hapmap]
rs4589882	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs4858094	0.88[TSI][hapmap]
rs4858095	0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[TSI][hapmap]
rs4858098	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4858553	0.88[TSI][hapmap]
rs4858561	0.91[JPT][hapmap]
rs4858567	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs4858569	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5023610	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6550814	0.91[ASN][1000 genomes]
rs6550815	0.94[ASN][1000 genomes]
rs6550819	0.90[ASN][1000 genomes]
rs6550823	0.91[CHB][hapmap];0.89[CHD][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs6762238	0.86[EUR][1000 genomes]
rs6779476	0.80[CEU][hapmap];0.90[TSI][hapmap]
rs6794922	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs6807856	0.88[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs7371944	0.81[MEX][hapmap];0.90[TSI][hapmap]
rs7431301	0.89[ASN][1000 genomes]
rs7646930	0.91[JPT][hapmap]
rs9831760	0.91[JPT][hapmap]
rs9842907	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs9845287	0.88[TSI][hapmap]
rs9853532	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9882735	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7636810	C3orf48	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23959600-23969400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:23960200-23969400	Weak transcription	Esophagus	oesophagus
3	chr3:23961800-23972800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:23961800-23980200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:23962000-23968200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:23962000-23968400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:23962000-23968800	Weak transcription	NHEK	skin
8	chr3:23962000-23969000	Weak transcription	Fetal Brain Male	brain
9	chr3:23962000-23969000	Weak transcription	Fetal Kidney	kidney
10	chr3:23962000-23969400	Weak transcription	Pancreas	Pancrea
11	chr3:23962000-23969600	Weak transcription	Gastric	stomach
12	chr3:23962000-23970000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:23962000-23972800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:23962000-23974800	Weak transcription	Brain Substantia Nigra	brain
15	chr3:23962000-23977800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:23962000-23985600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:23962200-23967800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:23962200-23968800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:23962200-23969000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:23962200-23970000	Weak transcription	Hela-S3	cervix
21	chr3:23962400-23968800	Weak transcription	HepG2	liver
22	chr3:23962400-23968800	Weak transcription	NHDF-Ad	bronchial
23	chr3:23962600-23970000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:23962800-23968800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:23963000-23968000	Weak transcription	Primary B cells from cord blood	blood
26	chr3:23963000-23968400	Weak transcription	A549	lung
27	chr3:23963000-23968800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:23963000-23975200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:23963200-23969200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:23963200-23973200	Weak transcription	GM12878-XiMat	blood
31	chr3:23963200-23976000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:23963600-23967800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr3:23963600-23968200	Weak transcription	Brain Angular Gyrus	brain
34	chr3:23963600-23973200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr3:23963800-23968000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:23963800-23968000	Weak transcription	Left Ventricle	heart
37	chr3:23963800-23968000	Weak transcription	Right Ventricle	heart
38	chr3:23963800-23968200	Weak transcription	Brain Anterior Caudate	brain
39	chr3:23963800-23968200	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:23963800-23968400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:23963800-23968800	Weak transcription	Fetal Lung	lung
42	chr3:23963800-23969000	Weak transcription	Adipose Nuclei	Adipose
43	chr3:23963800-23969400	Weak transcription	Thymus	Thymus
44	chr3:23963800-23970000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:23963800-23970600	Weak transcription	Primary T cells from cord blood	blood
46	chr3:23963800-23971000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:23963800-23973000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:23963800-23978400	Weak transcription	Aorta	Aorta
49	chr3:23964000-23968400	Weak transcription	Liver	Liver
50	chr3:23964000-23968800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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