Variant report

Variant	rs2289472
Chromosome Location	chr2:234182240-234182241
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234177414..234182460-chr2:234196864..234199879,7	MCF-7	breast:
2	chr2:234179437..234182271-chr2:234185909..234188121,2	MCF-7	breast:
3	chr2:234180205..234182361-chr2:234295517..234298044,2	MCF-7	breast:
4	chr2:234179520..234182515-chr2:234197814..234200700,2	MCF-7	breast:
5	chr2:234180075..234182326-chr2:234188683..234190200,2	MCF-7	breast:
6	chr2:234178234..234182601-chr2:234261429..234266540,8	MCF-7	breast:
7	chr2:234161285..234164496-chr2:234179412..234182858,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077044	Chromatin interaction
ENSG00000243637	Chromatin interaction
ENSG00000085978	Chromatin interaction
ENSG00000251791	Chromatin interaction
ENSG00000259793	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10164737	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10165561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10167613	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10178603	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10186850	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10187752	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10187822	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10192579	0.81[ASN][1000 genomes]
rs10192702	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10195395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10196794	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199278	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203952	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10206299	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10210302	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1045100	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10929322	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10929325	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10929326	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11679791	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11680089	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680130	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11687982	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11688431	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11690131	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11694081	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12162308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692250	0.81[ASN][1000 genomes]
rs12692254	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13003866	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13009506	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13015823	0.82[JPT][hapmap]
rs13035837	0.83[JPT][hapmap]
rs13391356	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411660	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13412102	0.81[ASN][1000 genomes]
rs13418066	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1441092	0.83[JPT][hapmap]
rs1596017	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2119505	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][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]
rs2241880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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]
rs2289474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289477	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.91[YRI][hapmap]
rs28454240	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2880080	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34123137	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34701569	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35300242	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36001488	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762588	0.83[JPT][hapmap]
rs3792106	0.95[CHB][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs3792108	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792109	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816234	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828309	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55835501	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56049444	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56227616	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6431654	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6431660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6431661	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705964	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738490	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745825	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559194	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[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	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2289472	B3GNT7	cis	cerebellum	SCAN
rs2289472	SCARNA5	cis	parietal	SCAN
rs2289472	ATG16L1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234162200-234205200	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr2:234162200-234205200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr2:234162400-234192000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr2:234162400-234196400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:234162400-234205200	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr2:234162400-234205400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:234162600-234188600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:234162600-234192400	Strong transcription	Osteobl	bone
9	chr2:234162600-234205000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:234162600-234205200	Strong transcription	Fetal Muscle Leg	muscle
11	chr2:234162800-234194000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:234162800-234197000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:234162800-234205600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:234163000-234192200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:234163000-234192200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr2:234163200-234188000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr2:234163200-234188800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:234163200-234206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:234163800-234188600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:234163800-234189000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr2:234164200-234205400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:234164200-234205400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:234164400-234192000	Strong transcription	NH-A	brain
24	chr2:234164400-234196800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:234164400-234197200	Strong transcription	Adipose Nuclei	Adipose
26	chr2:234164600-234190400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:234164600-234192000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:234164600-234192200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:234164600-234206000	Strong transcription	HepG2	liver
30	chr2:234164800-234195800	Strong transcription	Fetal Intestine Large	intestine
31	chr2:234165000-234192200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:234165000-234206000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:234165200-234205400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:234165400-234192000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr2:234166200-234191800	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr2:234166600-234189000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:234166800-234206000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:234169000-234185200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:234169400-234197200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:234169800-234192000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:234171200-234191800	Strong transcription	HSMM	muscle
42	chr2:234172200-234204800	Strong transcription	Placenta	Placenta
43	chr2:234173000-234186000	Weak transcription	Fetal Heart	heart
44	chr2:234174000-234196000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:234176400-234187400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:234176800-234207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:234177000-234182600	Weak transcription	NHLF	lung
48	chr2:234177000-234206000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:234177200-234192000	Strong transcription	HMEC	breast
50	chr2:234177200-234205400	Strong transcription	Dnd41	blood

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