Variant report

Variant	rs9842968
Chromosome Location	chr3:100500860-100500861
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	chr3:100494124..100496299-chr3:100500365..100501965,2	MCF-7	breast:
2	chr3:100493675..100497867-chr3:100498582..100501450,3	K562	blood:

Variant related genes	Relation type
ENSG00000154175	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11716316	0.85[JPT][hapmap]
rs12496951	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs12696195	0.86[CHB][hapmap]
rs13433770	0.82[CHB][hapmap]
rs1394077	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1503839	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs1503845	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs16842822	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs16842845	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1847391	0.82[JPT][hapmap]
rs3736534	0.87[CHD][hapmap]
rs544500	0.87[CHD][hapmap]
rs754462	0.83[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7609779	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7612334	0.84[JPT][hapmap]
rs7613610	0.80[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7632038	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7642942	0.91[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs764684	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs9824346	0.82[JPT][hapmap]
rs983474	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850273	0.88[ASW][hapmap];0.80[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs989793	0.84[JPT][hapmap];0.91[YRI][hapmap]
rs989794	0.82[JPT][hapmap];0.88[YRI][hapmap]
rs989795	0.84[CHD][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9842968	FAM55C	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
2	chr3:100469800-100501400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:100471800-100502000	Weak transcription	Brain Anterior Caudate	brain
4	chr3:100474400-100501200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:100475600-100520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:100478800-100502000	Weak transcription	Psoas Muscle	Psoas
7	chr3:100488600-100504600	Weak transcription	Adipose Nuclei	Adipose
8	chr3:100489800-100504800	Weak transcription	Left Ventricle	heart
9	chr3:100492400-100501000	Strong transcription	Stomach Smooth Muscle	stomach
10	chr3:100494800-100501600	Weak transcription	HMEC	breast
11	chr3:100494800-100523400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:100495000-100501000	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:100496200-100504200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:100496800-100501200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:100496800-100511200	Weak transcription	Aorta	Aorta
16	chr3:100497200-100501000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:100497200-100501400	Weak transcription	Fetal Intestine Large	intestine
18	chr3:100497200-100504400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:100498200-100501400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:100498200-100502400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr3:100498200-100502800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:100498600-100503000	Enhancers	NHDF-Ad	bronchial
23	chr3:100499000-100504400	Weak transcription	Ovary	ovary
24	chr3:100500000-100501800	Enhancers	NHEK	skin
25	chr3:100500000-100502400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:100500000-100503000	Genic enhancers	Osteobl	bone
27	chr3:100500200-100501200	Enhancers	HSMM	muscle
28	chr3:100500200-100502200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:100500200-100502200	Enhancers	NH-A	brain
30	chr3:100500200-100503200	Strong transcription	HSMMtube	muscle
31	chr3:100500400-100501200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:100500400-100502200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:100500400-100502200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:100500400-100502400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:100500400-100502400	Enhancers	NHLF	lung
36	chr3:100500400-100503000	Genic enhancers	Fetal Muscle Leg	muscle
37	chr3:100500600-100502400	Enhancers	Fetal Lung	lung
38	chr3:100500800-100501400	Genic enhancers	Fetal Stomach	stomach
39	chr3:100500800-100501600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:100500800-100502200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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