Variant report

Variant	rs2510777
Chromosome Location	chr4:95460949-95460950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95460434..95462251-chr4:95467361..95469680,2	MCF-7	breast:
2	chr4:95389173..95390941-chr4:95459071..95461024,2	K562	blood:
3	chr4:95451315..95454000-chr4:95460159..95462503,3	MCF-7	breast:
4	chr4:95460565..95462692-chr4:95465018..95467575,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10019142	0.83[ASN][1000 genomes]
rs10033326	0.82[CHB][hapmap]
rs10034824	0.94[CHB][hapmap]
rs1032420	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500426	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs12639623	0.81[CHD][hapmap]
rs12645971	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13110115	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13143502	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13146878	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17378777	0.80[MEX][hapmap]
rs1972011	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433320	0.83[MEX][hapmap]
rs2433322	0.80[MEX][hapmap]
rs2433327	0.82[MEX][hapmap]
rs2438140	0.82[MEX][hapmap]
rs2452008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452010	0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2452563	0.81[CEU][hapmap]
rs2452569	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2452570	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452572	0.85[ASN][1000 genomes]
rs2452574	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2452575	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2452576	0.80[ASN][1000 genomes]
rs2452580	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452582	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452584	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452585	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452586	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452589	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2510769	0.82[CHB][hapmap]
rs2510772	0.93[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510774	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2510775	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2510776	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510779	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2510780	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2510781	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2510793	0.81[CEU][hapmap]
rs28740868	0.86[ASN][1000 genomes]
rs3792666	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805263	0.81[CHB][hapmap]
rs3805266	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs3805285	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3843444	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4634230	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs4699505	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs6854173	0.82[CHB][hapmap]
rs7662466	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs766520	0.84[CEU][hapmap]
rs774984	0.82[MEX][hapmap]
rs902981	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2510777	PDLIM5	cis	parietal	SCAN
rs2510777	FAM190A	cis	cerebellum	SCAN
rs2510777	ATOH1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:95442000-95469600	Weak transcription	Primary T cells from cord blood	blood
3	chr4:95449200-95470200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:95450400-95465800	Weak transcription	Lung	lung
5	chr4:95453800-95465400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:95454600-95462600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr4:95456200-95463200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr4:95456400-95462800	Enhancers	HSMMtube	muscle
9	chr4:95456800-95465000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:95456800-95469800	Weak transcription	Ovary	ovary
11	chr4:95456800-95470200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:95457000-95469800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:95457400-95461400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:95457400-95461600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:95457400-95462000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:95457400-95462800	Weak transcription	Left Ventricle	heart
17	chr4:95457400-95465800	Weak transcription	Pancreas	Pancrea
18	chr4:95457400-95469800	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:95457400-95470000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:95457400-95485400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:95457600-95465600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:95457800-95461200	Enhancers	Fetal Heart	heart
23	chr4:95457800-95466400	Weak transcription	Brain Substantia Nigra	brain
24	chr4:95458000-95461600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:95458000-95469800	Weak transcription	Small Intestine	intestine
26	chr4:95458000-95480400	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:95458200-95461600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:95458200-95462400	Weak transcription	Right Ventricle	heart
29	chr4:95458200-95465600	Weak transcription	NHLF	lung
30	chr4:95458200-95483000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:95458200-95488800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr4:95458400-95461000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr4:95458400-95461000	Enhancers	HUVEC	blood vessel
34	chr4:95458400-95461600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:95458400-95461800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr4:95458400-95461800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr4:95458400-95465200	Weak transcription	HepG2	liver
38	chr4:95458400-95468600	Weak transcription	Liver	Liver
39	chr4:95458400-95469800	Weak transcription	Fetal Intestine Large	intestine
40	chr4:95459000-95461600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:95459000-95465200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr4:95459000-95473000	Weak transcription	Fetal Kidney	kidney
43	chr4:95459000-95480400	Weak transcription	Adipose Nuclei	Adipose
44	chr4:95459400-95461400	Enhancers	Placenta Amnion	Placenta Amnion
45	chr4:95459600-95461400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:95459600-95461800	Weak transcription	A549	lung
47	chr4:95459600-95462400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:95459600-95462600	Weak transcription	Fetal Intestine Small	intestine
49	chr4:95459600-95463000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:95459600-95464600	Weak transcription	HSMM	muscle

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