Variant report

Variant	rs9841110
Chromosome Location	chr3:49492481-49492482
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49491388..49494409-chr3:49505891..49508605,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10212296	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1050088	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1050450	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10865955	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130192	1.00[JPT][hapmap]
rs11130193	0.83[ASN][1000 genomes]
rs11130196	0.90[ASN][1000 genomes]
rs11130199	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11130202	0.82[ASN][1000 genomes]
rs11130203	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11706370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11708955	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11709525	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs11711485	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711536	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11712569	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11713474	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11716974	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11719996	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11720264	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11720597	0.81[EUR][1000 genomes]
rs11919311	0.86[JPT][hapmap]
rs11922013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11926781	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12330269	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489092	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13062429	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13079082	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13079643	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13086611	0.84[AMR][1000 genomes]
rs13087851	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13090388	0.89[AMR][1000 genomes]
rs1464566	1.00[JPT][hapmap]
rs1464567	1.00[JPT][hapmap]
rs1464568	1.00[JPT][hapmap]
rs1568661	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17080528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17650792	1.00[JPT][hapmap]
rs1800668	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1801143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1873625	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs1873626	0.88[JPT][hapmap]
rs1987628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2172252	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs2312461	0.82[ASN][1000 genomes]
rs2329020	0.86[JPT][hapmap]
rs34196454	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34293138	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34363169	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34427167	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34588335	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34762726	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs35115732	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35169793	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35261698	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35701831	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs35999162	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811697	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3811699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3870337	0.82[ASN][1000 genomes]
rs3870338	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3877784	0.82[ASN][1000 genomes]
rs3924462	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3926569	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4283605	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs4625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855836	0.82[ASN][1000 genomes]
rs4855839	1.00[JPT][hapmap]
rs4855842	1.00[JPT][hapmap]
rs4855852	0.86[JPT][hapmap]
rs4855859	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4855861	0.82[ASN][1000 genomes]
rs4855864	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4855866	0.92[ASN][1000 genomes]
rs4855873	1.00[JPT][hapmap]
rs4855877	1.00[JPT][hapmap]
rs59152804	0.86[ASN][1000 genomes]
rs6446264	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6446272	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6446277	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67216675	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67485053	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6766131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766581	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6770670	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs6779524	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6782577	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs6784820	1.00[JPT][hapmap]
rs6793308	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6797664	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6803222	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs6809216	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71324962	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71615484	0.84[ASN][1000 genomes]
rs7622302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7623659	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7630869	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7633271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637999	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7643845	0.82[ASN][1000 genomes]
rs7645445	0.90[ASN][1000 genomes]
rs7646366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7648841	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs885592	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9811982	1.00[CEU][hapmap]
rs9812791	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9814873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9818590	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9821311	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9827021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9827708	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9837027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9837341	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs9850072	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9853683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9858280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9858418	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9859556	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9871380	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs9878943	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9841110	FAM212A	cis	Muscle Skeletal	GTEx
rs9841110	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs9841110	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49482000-49498200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:49486600-49498600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:49490200-49494200	Enhancers	Fetal Muscle Trunk	muscle
4	chr3:49490600-49506600	Enhancers	Fetal Muscle Leg	muscle
5	chr3:49491200-49495000	Enhancers	Hela-S3	cervix
6	chr3:49491400-49493400	Enhancers	HepG2	liver
7	chr3:49491400-49494200	Enhancers	Right Ventricle	heart
8	chr3:49491800-49492600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:49491800-49492800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:49491800-49493000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:49491800-49493000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:49491800-49493000	Enhancers	Pancreas	Pancrea
13	chr3:49491800-49493800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:49491800-49494400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:49491800-49495000	Enhancers	HSMMtube	muscle
16	chr3:49491800-49506200	Enhancers	Placenta	Placenta
17	chr3:49492000-49492600	Enhancers	Stomach Mucosa	stomach
18	chr3:49492000-49492600	Enhancers	Stomach Smooth Muscle	stomach
19	chr3:49492000-49492800	Enhancers	Fetal Kidney	kidney
20	chr3:49492000-49492800	Enhancers	Lung	lung
21	chr3:49492000-49492800	Enhancers	Right Atrium	heart
22	chr3:49492000-49493400	Enhancers	Adipose Nuclei	Adipose
23	chr3:49492000-49493400	Enhancers	Left Ventricle	heart
24	chr3:49492000-49493400	Enhancers	Psoas Muscle	Psoas
25	chr3:49492000-49493600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:49492000-49494000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:49492000-49494200	Enhancers	Fetal Heart	heart
28	chr3:49492000-49495000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:49492000-49495000	Enhancers	HSMM	muscle
30	chr3:49492200-49492800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr3:49492200-49492800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr3:49492200-49492800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:49492200-49492800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:49492200-49492800	Weak transcription	Spleen	Spleen
35	chr3:49492200-49493000	Enhancers	H9 Cell Line	embryonic stem cell
36	chr3:49492200-49493000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:49492200-49493000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:49492200-49493000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:49492200-49493000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr3:49492200-49493200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:49492200-49493200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:49492200-49493200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:49492200-49493200	Enhancers	A549	lung
44	chr3:49492200-49494200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:49492200-49494200	Enhancers	HMEC	breast
46	chr3:49492200-49495000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr3:49492400-49492600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr3:49492400-49492800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:49492400-49493000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr3:49492400-49493000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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