Variant report

Variant	rs3099990
Chromosome Location	chr2:39060078-39060079
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39060039..39062647-chr2:39091366..39093415,2	K562	blood:
2	chr2:39053503..39057037-chr2:39058758..39062643,3	K562	blood:
3	chr2:38973416..38975582-chr2:39059535..39061861,2	MCF-7	breast:
4	chr2:39053503..39055563-chr2:39060007..39062643,2	K562	blood:
5	chr2:38976872..38979840-chr2:39056753..39060826,5	K562	blood:
6	chr2:38976968..38979836-chr2:39057307..39060764,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1010859	0.88[JPT][hapmap]
rs10865143	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11898812	0.83[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12618118	0.83[CHB][hapmap]
rs12621103	0.90[CHB][hapmap]
rs1979143	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3097713	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs3097714	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs3099961	0.85[ASN][1000 genomes]
rs3099965	0.85[ASN][1000 genomes]
rs3099968	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099971	0.82[ASN][1000 genomes]
rs3099975	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3099977	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3099980	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3099981	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3099992	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3100000	1.00[JPT][hapmap]
rs3112142	0.87[CEU][hapmap];0.81[CHB][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112143	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3112150	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112159	0.88[JPT][hapmap]
rs3112163	1.00[JPT][hapmap]
rs3112178	0.88[JPT][hapmap]
rs3112183	0.81[CHB][hapmap]
rs3112184	0.83[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3112186	0.82[ASN][1000 genomes]
rs3112188	0.83[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3112189	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3112191	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3112192	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3112194	0.84[ASN][1000 genomes]
rs3112196	0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs3112198	0.81[ASN][1000 genomes]
rs3112204	0.85[ASN][1000 genomes]
rs3134637	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs4670268	0.86[JPT][hapmap]
rs6544175	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6717670	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs756338	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
3	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
5	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:39038800-39102200	Weak transcription	Gastric	stomach
8	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
10	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
12	chr2:39040000-39069000	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:39042800-39063000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:39042800-39080600	Weak transcription	Small Intestine	intestine
15	chr2:39043600-39079800	Weak transcription	Right Ventricle	heart
16	chr2:39046000-39073200	Weak transcription	Pancreas	Pancrea
17	chr2:39046200-39070200	Weak transcription	NHLF	lung
18	chr2:39048400-39060800	Strong transcription	Fetal Stomach	stomach
19	chr2:39050400-39062800	Weak transcription	Thymus	Thymus
20	chr2:39050400-39063800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:39050400-39072800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:39050400-39079800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:39050400-39079800	Weak transcription	Spleen	Spleen
24	chr2:39050400-39088000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:39051000-39068600	Weak transcription	HMEC	breast
26	chr2:39052000-39061800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:39052200-39068600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:39053200-39068600	Weak transcription	Brain Substantia Nigra	brain
29	chr2:39053200-39069600	Weak transcription	HUVEC	blood vessel
30	chr2:39053600-39062400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:39053800-39060600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:39053800-39060600	Weak transcription	Fetal Kidney	kidney
33	chr2:39053800-39061800	Weak transcription	Fetal Lung	lung
34	chr2:39053800-39062400	Weak transcription	Left Ventricle	heart
35	chr2:39053800-39062800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:39053800-39063000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:39053800-39063800	Weak transcription	Liver	Liver
38	chr2:39053800-39064600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:39053800-39068200	Weak transcription	HSMM	muscle
40	chr2:39053800-39068400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:39053800-39068600	Weak transcription	Aorta	Aorta
42	chr2:39053800-39068800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:39053800-39080200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:39053800-39080600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:39054000-39060200	Weak transcription	Brain Hippocampus Middle	brain
46	chr2:39054000-39060600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:39054000-39061400	Weak transcription	Fetal Thymus	thymus
48	chr2:39054000-39061800	Weak transcription	NHEK	skin
49	chr2:39054000-39062000	Weak transcription	Primary B cells from cord blood	blood
50	chr2:39054000-39062000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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