Variant report

Variant	rs2624847
Chromosome Location	chr3:50174197-50174198
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50171634..50174420-chr3:50273113..50275042,2	MCF-7	breast:
2	chr3:50172563..50177055-chr3:50182695..50185570,4	MCF-7	breast:
3	chr3:50171724..50175454-chr3:50183857..50186951,3	K562	blood:
4	chr3:50171431..50173846-chr3:50174182..50176296,2	K562	blood:

Variant related genes	Relation type
ENSG00000114353	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10049087	0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11130228	1.00[JPT][hapmap]
rs11130233	1.00[JPT][hapmap]
rs12496973	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs12634780	0.82[JPT][hapmap]
rs13060128	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs17657664	0.82[JPT][hapmap]
rs17657688	0.82[JPT][hapmap]
rs2008877	0.82[GIH][hapmap];0.92[JPT][hapmap]
rs2013208	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2071206	0.88[ASN][1000 genomes]
rs2071207	0.90[ASN][1000 genomes]
rs2236939	0.82[JPT][hapmap]
rs2240326	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2240327	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2240328	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2240329	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2245365	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2247510	0.82[JPT][hapmap]
rs2252833	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2301166	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2352969	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2353579	1.00[JPT][hapmap]
rs2526743	0.83[ASN][1000 genomes]
rs2526747	0.82[JPT][hapmap]
rs2526748	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2526751	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2526754	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2624816	0.83[ASN][1000 genomes]
rs2624819	0.82[JPT][hapmap]
rs2624821	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2624822	0.82[JPT][hapmap]
rs2624825	0.85[ASN][1000 genomes]
rs2624834	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2624843	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2624853	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2681779	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2856234	0.85[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2856236	0.83[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs2883057	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs34831713	0.83[ASN][1000 genomes]
rs3733133	0.86[ASN][1000 genomes]
rs3774733	1.00[JPT][hapmap]
rs3774734	0.82[JPT][hapmap]
rs4688686	0.93[ASN][1000 genomes]
rs4688689	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs4688690	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs4688753	0.82[JPT][hapmap]
rs4688755	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs4688758	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6446193	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6446202	0.82[JPT][hapmap]
rs6762477	0.82[JPT][hapmap]
rs6765484	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6772095	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6792892	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7061	0.82[JPT][hapmap]
rs739431	0.82[JPT][hapmap]
rs7428430	0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7430334	0.82[JPT][hapmap]
rs7621026	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7621352	1.00[JPT][hapmap]
rs7628058	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7642692	0.82[JPT][hapmap]
rs7642934	0.81[ASN][1000 genomes]
rs9311446	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9814664	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9856572	0.83[ASN][1000 genomes]
rs9861216	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs9866695	0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv818139	chr3:50144951-50174572	Weak transcription Strong transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
8	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
11	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
12	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
13	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
14	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
15	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
16	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
17	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2624847	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2624847	WDR6	cis	parietal	SCAN
rs2624847	CYB561D2	cis	cerebellum	SCAN
rs2624847	NCKIPSD	cis	parietal	SCAN
rs2624847	PAX1	trans	parietal	SCAN
rs2624847	C3orf78	cis	parietal	SCAN
rs2624847	RBM6	cis	parietal	SCAN
rs2624847	RBM6	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50151000-50176400	Weak transcription	Right Atrium	heart
2	chr3:50164400-50174600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:50164600-50174200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:50168200-50175200	Weak transcription	Spleen	Spleen
5	chr3:50170400-50175600	Weak transcription	Fetal Brain Male	brain
6	chr3:50170600-50175400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:50170600-50175800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:50170800-50174200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:50171200-50174200	Weak transcription	Brain Anterior Caudate	brain
10	chr3:50171200-50178400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:50171600-50175000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:50172400-50176600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr3:50172600-50174400	Weak transcription	Esophagus	oesophagus
14	chr3:50172600-50175200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:50173200-50178000	Enhancers	Fetal Lung	lung
16	chr3:50173400-50174200	Bivalent Enhancer	HepG2	liver
17	chr3:50173400-50174600	Enhancers	Adipose Nuclei	Adipose
18	chr3:50173400-50175000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:50173400-50176600	Enhancers	Fetal Stomach	stomach
20	chr3:50173400-50178200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr3:50173600-50175600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:50173600-50176800	Enhancers	Fetal Muscle Leg	muscle
23	chr3:50173600-50177400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:50173600-50177400	Enhancers	Fetal Kidney	kidney
25	chr3:50173800-50175000	Weak transcription	Fetal Brain Female	brain
26	chr3:50173800-50175800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:50173800-50177400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:50173800-50177800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:50174000-50174600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:50174000-50174600	Enhancers	Psoas Muscle	Psoas
31	chr3:50174000-50176400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:50174000-50177200	Enhancers	Placenta	Placenta

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