Variant report

Variant	rs2850356
Chromosome Location	chr4:102211922-102211923
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	chr4:102211391..102213772-chr4:102219486..102221204,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10007902	0.82[JPT][hapmap]
rs1031033	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1031034	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1348161	0.95[JPT][hapmap]
rs1441433	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1530259	0.95[JPT][hapmap]
rs1549513	0.80[JPT][hapmap]
rs1549515	0.84[JPT][hapmap]
rs1549516	0.80[JPT][hapmap]
rs1561719	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2028475	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2099813	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583389	0.95[JPT][hapmap]
rs2583392	0.95[JPT][hapmap]
rs2583394	0.95[JPT][hapmap]
rs2583395	0.95[JPT][hapmap]
rs2583398	0.95[JPT][hapmap]
rs2583399	0.95[JPT][hapmap]
rs2583400	0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2583401	0.93[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2583402	0.93[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583406	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2583410	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850326	0.95[JPT][hapmap]
rs2850332	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850339	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850344	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850348	0.97[EUR][1000 genomes]
rs2850349	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850350	0.93[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes]
rs2850351	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850352	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850354	0.92[CEU][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes]
rs2850355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850357	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850358	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850360	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2850366	0.81[ASN][1000 genomes]
rs2850367	0.95[JPT][hapmap]
rs2850368	0.81[ASN][1000 genomes]
rs2850369	0.86[JPT][hapmap]
rs2850370	0.95[JPT][hapmap]
rs2850371	0.95[JPT][hapmap]
rs2850954	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2850963	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850967	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850969	0.93[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850974	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850975	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850976	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28664200	0.81[ASN][1000 genomes]
rs4452435	0.80[JPT][hapmap]
rs755961	0.93[CEU][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes]
rs920559	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs920560	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962384	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102201000-102213000	Weak transcription	Fetal Heart	heart
2	chr4:102201200-102218200	Weak transcription	NHEK	skin
3	chr4:102201400-102214200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:102205000-102212600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:102207000-102216600	Weak transcription	NH-A	brain
6	chr4:102207200-102212000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:102207400-102212000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:102207400-102212000	Weak transcription	Gastric	stomach
9	chr4:102207400-102214200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:102207400-102214200	Weak transcription	Esophagus	oesophagus
11	chr4:102207600-102226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:102208000-102212400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:102208600-102212800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr4:102208600-102212800	Enhancers	Brain Anterior Caudate	brain
15	chr4:102208600-102213200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr4:102209400-102212000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:102209400-102212000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:102209400-102214200	Weak transcription	Aorta	Aorta
19	chr4:102209400-102214400	Weak transcription	Right Ventricle	heart
20	chr4:102209800-102212000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr4:102209800-102212400	Weak transcription	A549	lung
22	chr4:102209800-102214400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:102210000-102212600	Enhancers	Primary T cells from cord blood	blood
24	chr4:102210200-102212000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:102210200-102212000	Weak transcription	Pancreas	Pancrea
26	chr4:102210200-102212200	Weak transcription	Brain Angular Gyrus	brain
27	chr4:102210200-102212800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:102210200-102213600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:102210200-102214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:102210200-102215600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr4:102210200-102225800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:102210400-102212000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:102210600-102212000	Weak transcription	Brain Substantia Nigra	brain
34	chr4:102210600-102212000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:102210600-102212000	Weak transcription	Osteobl	bone
36	chr4:102210600-102212200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:102210600-102212600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:102210600-102214200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr4:102210600-102215800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:102210800-102212400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:102210800-102212600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr4:102210800-102212800	Enhancers	Primary B cells from peripheral blood	blood
43	chr4:102211000-102212200	Enhancers	Right Atrium	heart
44	chr4:102211000-102212600	Enhancers	Psoas Muscle	Psoas
45	chr4:102211000-102213200	Enhancers	Small Intestine	intestine
46	chr4:102211000-102214200	Enhancers	Ovary	ovary
47	chr4:102211200-102212000	Weak transcription	Lung	lung
48	chr4:102211200-102215400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:102211200-102215600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:102211200-102219000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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