Variant report

Variant	rs10028164
Chromosome Location	chr4:27004011-27004012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:27003891-27004015	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
STIM2	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10031905	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1035075	1.00[EUR][1000 genomes]
rs1860981	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2192241	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2309497	1.00[EUR][1000 genomes]
rs28489605	1.00[EUR][1000 genomes]
rs4129747	1.00[ASW][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4140681	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4599399	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4692016	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4692017	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4692018	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4692135	0.93[AMR][1000 genomes]
rs4692138	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55646519	1.00[EUR][1000 genomes]
rs56001106	1.00[EUR][1000 genomes]
rs56810203	1.00[EUR][1000 genomes]
rs57668778	1.00[EUR][1000 genomes]
rs57810647	1.00[EUR][1000 genomes]
rs59530500	1.00[EUR][1000 genomes]
rs59678983	1.00[EUR][1000 genomes]
rs61084398	1.00[EUR][1000 genomes]
rs6448489	0.88[AMR][1000 genomes]
rs6448490	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6841079	1.00[EUR][1000 genomes]
rs6858361	1.00[EUR][1000 genomes]
rs73116642	1.00[EUR][1000 genomes]
rs73116643	1.00[EUR][1000 genomes]
rs73116645	1.00[EUR][1000 genomes]
rs73116652	1.00[EUR][1000 genomes]
rs73116653	1.00[EUR][1000 genomes]
rs73116655	1.00[EUR][1000 genomes]
rs73116657	1.00[EUR][1000 genomes]
rs73116660	1.00[EUR][1000 genomes]
rs73116665	1.00[EUR][1000 genomes]
rs73116670	1.00[EUR][1000 genomes]
rs73116672	1.00[EUR][1000 genomes]
rs73116675	1.00[EUR][1000 genomes]
rs7670520	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7688601	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs887792	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs887794	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9790760	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994911	0.88[AMR][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	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1000568	chr4:26886920-27049554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
2	chr4:26980400-27019400	Weak transcription	Left Ventricle	heart
3	chr4:26985400-27019400	Weak transcription	Esophagus	oesophagus
4	chr4:26989000-27010000	Weak transcription	Thymus	Thymus
5	chr4:26989000-27010400	Weak transcription	Fetal Thymus	thymus
6	chr4:26989400-27024800	Weak transcription	Psoas Muscle	Psoas
7	chr4:26989600-27027000	Weak transcription	HepG2	liver
8	chr4:26994200-27004600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:26994800-27004600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:26994800-27005200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:26994800-27011000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:26995000-27004200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr4:26995000-27004600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:26995000-27004600	Weak transcription	Small Intestine	intestine
15	chr4:26995000-27019000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:26995000-27028200	Weak transcription	Pancreas	Pancrea
17	chr4:26995200-27004600	Weak transcription	HMEC	breast
18	chr4:26995200-27006600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:26995400-27009800	Weak transcription	Adipose Nuclei	Adipose
20	chr4:26995600-27004600	Weak transcription	NH-A	brain
21	chr4:26995600-27004800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:26996200-27004200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:26996200-27015400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:26996400-27005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr4:26996400-27007600	Weak transcription	Brain Angular Gyrus	brain
26	chr4:26996400-27026200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:26996600-27004600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:26996600-27007600	Weak transcription	Ovary	ovary
29	chr4:26996600-27011800	Weak transcription	Brain Anterior Caudate	brain
30	chr4:26996600-27018400	Weak transcription	Fetal Intestine Large	intestine
31	chr4:26996600-27019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:26996800-27007200	Weak transcription	Brain Substantia Nigra	brain
33	chr4:26996800-27019200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:26997000-27004400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr4:26997000-27007600	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:26997200-27004400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:26997200-27006400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:26997400-27004600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr4:26997400-27019200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:26997800-27004600	Weak transcription	Primary T cells from cord blood	blood
41	chr4:26998800-27004400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:26999200-27004400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:26999400-27004600	Weak transcription	Dnd41	blood
44	chr4:26999600-27005000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:27000400-27005400	Weak transcription	Osteobl	bone
46	chr4:27000600-27004600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:27001200-27029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:27001400-27005200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr4:27001600-27006800	Weak transcription	Liver	Liver
50	chr4:27001600-27019000	Weak transcription	Spleen	Spleen

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