Variant report

Variant	rs3088371
Chromosome Location	chr1:93826178-93826179
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93810776..93812361-chr1:93825332..93827504,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223745	Chromatin interaction
ENSG00000117505	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1079750	0.87[CEU][hapmap]
rs11164922	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11164930	0.87[CEU][hapmap]
rs11164940	0.85[CEU][hapmap]
rs11811006	0.82[EUR][1000 genomes]
rs12069440	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12096122	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12405666	0.81[EUR][1000 genomes]
rs12409621	0.81[EUR][1000 genomes]
rs12411095	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1582773	0.82[EUR][1000 genomes]
rs17109951	1.00[CEU][hapmap]
rs17109997	0.85[CEU][hapmap]
rs17131709	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs17131710	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17131718	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17131741	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17386609	0.81[EUR][1000 genomes]
rs1895903	0.82[EUR][1000 genomes]
rs2038698	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081568	0.81[EUR][1000 genomes]
rs2624437	0.85[CEU][hapmap]
rs4347219	0.81[EUR][1000 genomes]
rs57710451	0.82[EUR][1000 genomes]
rs60013975	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61101021	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66804824	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67998457	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72715394	0.81[EUR][1000 genomes]
rs72717337	0.81[EUR][1000 genomes]
rs72717354	0.81[EUR][1000 genomes]
rs72717374	0.81[EUR][1000 genomes]
rs72719185	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7339890	0.82[EUR][1000 genomes]
rs7539210	0.85[CEU][hapmap]
rs900310	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93812800-93831000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:93812800-93832200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:93813400-93840000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:93813400-93840400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:93815400-93839800	Weak transcription	Aorta	Aorta
6	chr1:93815600-93834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:93816000-93832200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:93816600-93841800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:93816800-93841200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:93817800-93832400	Weak transcription	Psoas Muscle	Psoas
11	chr1:93818000-93826400	Strong transcription	Placenta	Placenta
12	chr1:93818000-93835400	Weak transcription	Small Intestine	intestine
13	chr1:93818200-93826400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:93818200-93826600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:93818400-93826200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:93818400-93836000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:93818800-93827200	Strong transcription	Fetal Thymus	thymus
18	chr1:93818800-93837200	Weak transcription	Fetal Kidney	kidney
19	chr1:93819000-93828000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:93819000-93833200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:93819200-93826400	Strong transcription	HUVEC	blood vessel
22	chr1:93819400-93826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:93819400-93832000	Strong transcription	HSMM	muscle
24	chr1:93819400-93834600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr1:93819600-93826400	Strong transcription	NH-A	brain
26	chr1:93819600-93826600	Strong transcription	HepG2	liver
27	chr1:93819600-93830000	Strong transcription	HMEC	breast
28	chr1:93819800-93827000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:93819800-93827200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:93819800-93827600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:93819800-93829800	Strong transcription	NHDF-Ad	bronchial
32	chr1:93819800-93830800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:93820000-93826600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:93820000-93827200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:93820200-93828200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr1:93820600-93827400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:93820600-93837200	Weak transcription	Colonic Mucosa	Colon
38	chr1:93821000-93838800	Weak transcription	Ovary	ovary
39	chr1:93821200-93835200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:93822200-93835800	Strong transcription	Dnd41	blood
41	chr1:93822200-93840200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:93822600-93826200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr1:93823200-93826400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:93823800-93826400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
45	chr1:93823800-93827600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:93823800-93834600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr1:93824000-93830000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:93824000-93831000	Weak transcription	Fetal Brain Male	brain
49	chr1:93824200-93826600	Enhancers	Stomach Mucosa	stomach
50	chr1:93824200-93828600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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