Variant report

Variant	rs4725988
Chromosome Location	chr7:150791679-150791680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150790537..150793410-chr7:150796885..150799076,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10085680	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10244332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10273337	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1036061	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1036062	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1077122	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10952301	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10952302	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11766855	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11769150	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs12703112	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs13240966	0.87[ASN][1000 genomes]
rs13246833	0.87[ASN][1000 genomes]
rs34104727	1.00[ASN][1000 genomes]
rs34308016	1.00[ASN][1000 genomes]
rs4236428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4725989	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4725992	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725993	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62490310	0.82[EUR][1000 genomes]
rs62490311	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6464129	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6945607	0.86[EUR][1000 genomes]
rs6951528	0.88[GIH][hapmap]
rs6957724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970547	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970773	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7385751	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs749320	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7806979	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs891510	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
2	nsv889465	chr7:150640285-150800823	Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1028645	chr7:150643928-150806534	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
4	nsv539198	chr7:150643928-150879259	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv889476	chr7:150729212-150951819	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer 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	120 gene(s)	inside rSNPs	diseases
6	nsv889477	chr7:150731698-150837529	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv889478	chr7:150732812-150889527	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv831188	chr7:150735204-150912875	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers 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 target site	64 gene(s)	inside rSNPs	diseases
9	nsv889480	chr7:150736382-150797581	Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
10	nsv465214	chr7:150751590-150822192	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	nsv609012	chr7:150751590-150822192	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
12	nsv609013	chr7:150751590-150832913	Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
13	nsv465215	chr7:150762871-150825087	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	nsv609014	chr7:150762871-150825087	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv889481	chr7:150766799-150837529	Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	nsv889482	chr7:150766799-150851566	Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS 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	45 gene(s)	inside rSNPs	diseases
17	nsv889486	chr7:150775306-150891641	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4725988	SMARCD3	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150785000-150812000	Weak transcription	Aorta	Aorta
2	chr7:150786400-150808400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:150786600-150792600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:150786800-150799000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:150787000-150796600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:150787000-150799400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:150787200-150791800	Weak transcription	Esophagus	oesophagus
8	chr7:150787200-150792600	Enhancers	Adipose Nuclei	Adipose
9	chr7:150787200-150793000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:150787200-150793000	Weak transcription	HSMMtube	muscle
11	chr7:150787200-150793200	Weak transcription	Psoas Muscle	Psoas
12	chr7:150787200-150800600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:150787200-150801400	Weak transcription	NH-A	brain
14	chr7:150787400-150792200	Weak transcription	HMEC	breast
15	chr7:150787400-150800000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr7:150787400-150807800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:150787800-150792200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:150787800-150792400	Weak transcription	Ovary	ovary
19	chr7:150787800-150800000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:150787800-150801800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:150787800-150801800	Weak transcription	NHLF	lung
22	chr7:150788400-150800600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:150788600-150792400	Strong transcription	HepG2	liver
24	chr7:150788600-150807400	Weak transcription	Fetal Heart	heart
25	chr7:150788800-150792200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:150789000-150795600	Strong transcription	Fetal Intestine Small	intestine
27	chr7:150789000-150796600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:150789000-150796800	Weak transcription	Stomach Mucosa	stomach
29	chr7:150789000-150798600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr7:150789000-150800200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:150789000-150801400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr7:150789000-150815400	Weak transcription	GM12878-XiMat	blood
33	chr7:150789200-150791800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:150789200-150792400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:150789200-150796600	Weak transcription	Right Ventricle	heart
36	chr7:150789200-150801600	Weak transcription	Colonic Mucosa	Colon
37	chr7:150789200-150802400	Strong transcription	Fetal Stomach	stomach
38	chr7:150789400-150791800	Weak transcription	Brain Substantia Nigra	brain
39	chr7:150789400-150791800	Weak transcription	Spleen	Spleen
40	chr7:150789400-150792000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:150789400-150793600	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr7:150789400-150801600	Weak transcription	Pancreas	Pancrea
43	chr7:150789400-150807800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr7:150789600-150791800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr7:150789600-150792000	Weak transcription	A549	lung
46	chr7:150789600-150796600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:150789600-150807000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:150789800-150792400	Weak transcription	Left Ventricle	heart
49	chr7:150789800-150793000	Weak transcription	Placenta	Placenta
50	chr7:150789800-150800600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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