Variant report

Variant	rs4398571
Chromosome Location	chr4:159071004-159071005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159065591..159067245-chr4:159070446..159072937,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10517684	0.80[CEU][hapmap];0.89[CHD][hapmap]
rs10517688	0.94[CEU][hapmap];0.92[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10857307	0.85[CEU][hapmap];0.89[CHD][hapmap]
rs10857308	0.85[CEU][hapmap]
rs12511578	0.83[CEU][hapmap]
rs12650454	0.80[CEU][hapmap]
rs17036918	0.80[CEU][hapmap];0.89[CHD][hapmap]
rs17036921	0.89[CHD][hapmap]
rs17037003	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17037241	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2245735	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4129400	0.80[CEU][hapmap]
rs4460050	0.85[CEU][hapmap];0.89[CHD][hapmap]
rs4691449	0.85[CEU][hapmap];0.89[CHD][hapmap]
rs62335861	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62335862	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62335889	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62337014	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62337015	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6536298	0.84[CHD][hapmap]
rs6833295	0.92[JPT][hapmap]
rs7384	0.87[ASW][hapmap];0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv967692	chr4:159068843-159076875	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4398571	FLJ11155	cis	multi-tissue	Pritchard
rs4398571	FAM198B	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:159044800-159073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:159047000-159080200	Weak transcription	Right Ventricle	heart
4	chr4:159051800-159073000	Weak transcription	Fetal Stomach	stomach
5	chr4:159051800-159080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:159052000-159071400	Weak transcription	Adipose Nuclei	Adipose
7	chr4:159052200-159071400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:159052200-159072800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:159052600-159071200	Weak transcription	Fetal Intestine Small	intestine
10	chr4:159052600-159071400	Weak transcription	HSMMtube	muscle
11	chr4:159052600-159080200	Weak transcription	Left Ventricle	heart
12	chr4:159055600-159076200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:159059000-159077800	Weak transcription	Aorta	Aorta
14	chr4:159059400-159071800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:159059400-159076600	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:159060600-159071200	Weak transcription	Ovary	ovary
17	chr4:159060600-159071400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:159060600-159076600	Weak transcription	HMEC	breast
19	chr4:159062000-159077600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:159062600-159077800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:159062600-159083600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:159063200-159071600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:159063400-159078800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:159064000-159071800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:159066200-159076600	Weak transcription	Small Intestine	intestine
26	chr4:159066200-159076800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr4:159066400-159080400	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:159066600-159071400	Weak transcription	HepG2	liver
29	chr4:159066600-159072000	Weak transcription	HUVEC	blood vessel
30	chr4:159067400-159077200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:159067600-159073400	Strong transcription	HSMM	muscle
32	chr4:159068400-159078200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:159068600-159080400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:159068600-159080400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:159068600-159082000	Weak transcription	Brain Substantia Nigra	brain
36	chr4:159068800-159076200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:159068800-159079400	Weak transcription	Brain Angular Gyrus	brain
38	chr4:159068800-159081000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:159069400-159077000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:159070400-159071600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:159070600-159073400	Strong transcription	Fetal Intestine Large	intestine
42	chr4:159070600-159079800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr4:159070800-159074000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:159071000-159071200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:159071000-159071600	Weak transcription	Fetal Heart	heart
46	chr4:159071000-159072000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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