Variant report

Variant	rs1476122
Chromosome Location	chr4:143469236-143469237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143451539..143454827-chr4:143468974..143471578,3	MCF-7	breast:
2	chr4:143390493..143399629-chr4:143464669..143473703,24	MCF-7	breast:
3	chr4:143463931..143465579-chr4:143468036..143470044,2	MCF-7	breast:
4	chr4:143467061..143469661-chr4:143478956..143481210,2	MCF-7	breast:
5	chr4:143459017..143460718-chr4:143467557..143470331,2	MCF-7	breast:
6	chr4:143469197..143474225-chr4:143534708..143538333,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10013367	0.86[ASN][1000 genomes]
rs10519649	0.80[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11100748	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11100749	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11100750	0.86[ASN][1000 genomes]
rs1160379	0.82[ASN][1000 genomes]
rs11930912	0.84[EUR][1000 genomes]
rs11939291	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11943687	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12504375	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12504378	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12504770	0.86[EUR][1000 genomes]
rs13144094	0.84[ASN][1000 genomes]
rs1425518	0.95[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1425519	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1559709	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16998558	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16998560	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs17016344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17016354	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17016379	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17717651	0.86[EUR][1000 genomes]
rs1963849	0.87[ASN][1000 genomes]
rs1974940	0.86[ASN][1000 genomes]
rs2059510	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2059511	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2059513	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2217016	0.95[CEU][hapmap];0.92[CHB][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34007357	0.82[ASN][1000 genomes]
rs34223306	0.85[ASN][1000 genomes]
rs35854467	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4246729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4524461	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4975306	0.82[CEU][hapmap];0.82[GIH][hapmap];0.86[EUR][1000 genomes]
rs4975312	0.86[ASN][1000 genomes]
rs4975313	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4975314	0.86[ASN][1000 genomes]
rs4975316	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4975317	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975318	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57201046	0.87[ASN][1000 genomes]
rs57260347	0.87[ASN][1000 genomes]
rs58078405	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58899027	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59732892	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60951295	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61104737	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61142249	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6537109	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6537110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67078907	0.86[ASN][1000 genomes]
rs67311549	0.87[ASN][1000 genomes]
rs67900719	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6814775	0.87[ASN][1000 genomes]
rs6816875	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6826090	0.86[ASN][1000 genomes]
rs7655599	0.86[ASN][1000 genomes]
rs7671198	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs890191	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs890192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv461660	chr4:143437219-143538179	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv595605	chr4:143437219-143538179	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1476122	C7orf25	trans	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143461400-143471000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr4:143463000-143472200	Weak transcription	Aorta	Aorta
3	chr4:143463200-143470200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:143465200-143470600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:143465600-143470200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:143465600-143470200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:143465600-143470400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:143465600-143470800	Weak transcription	Stomach Mucosa	stomach
9	chr4:143465600-143472800	Weak transcription	Fetal Lung	lung
10	chr4:143465800-143470800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:143466000-143470400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:143466000-143470800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:143466000-143471200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:143466200-143470600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:143466600-143471000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:143466800-143470200	Weak transcription	Fetal Intestine Large	intestine
17	chr4:143467800-143470400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:143468200-143470200	Enhancers	NHEK	skin
19	chr4:143468200-143470600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:143468400-143469600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr4:143468400-143470400	Enhancers	HMEC	breast
22	chr4:143468400-143473400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:143468600-143472600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:143468600-143473200	Enhancers	Fetal Intestine Small	intestine
25	chr4:143468800-143480000	Weak transcription	Left Ventricle	heart
26	chr4:143469000-143469600	Enhancers	NH-A	brain
27	chr4:143469000-143469800	Enhancers	Fetal Heart	heart
28	chr4:143469000-143470800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr4:143469000-143473400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:143469200-143469400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:143469200-143469400	Enhancers	Psoas Muscle	Psoas
32	chr4:143469200-143469400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr4:143469200-143469400	Enhancers	Small Intestine	intestine
34	chr4:143469200-143469400	Enhancers	Osteobl	bone
35	chr4:143469200-143472600	Enhancers	Muscle Satellite Cultured Cells	--

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