Variant report

Variant	rs3100000
Chromosome Location	chr2:39090828-39090829
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39089505..39093700-chr2:39094409..39098372,5	K562	blood:
2	chr2:39086851..39091387-chr2:39094171..39096771,4	K562	blood:
3	chr2:39088675..39091170-chr2:39093044..39095216,2	MCF-7	breast:
4	chr2:39065831..39067433-chr2:39089862..39092131,2	K562	blood:
5	chr2:39082200..39083996-chr2:39090256..39092735,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163214	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1010859	0.88[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10865143	1.00[JPT][hapmap]
rs11124651	0.89[EUR][1000 genomes]
rs11681583	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11898812	1.00[JPT][hapmap]
rs12373604	0.91[EUR][1000 genomes]
rs12465365	0.81[EUR][1000 genomes]
rs12712625	0.89[CEU][hapmap]
rs12712626	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[EUR][1000 genomes]
rs12712627	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs13029388	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs13035182	0.87[AFR][1000 genomes]
rs1530852	0.81[CEU][hapmap]
rs17422748	0.88[AFR][1000 genomes]
rs1979143	1.00[JPT][hapmap]
rs2373469	0.85[AFR][1000 genomes]
rs2373471	0.85[AFR][1000 genomes]
rs3097713	0.88[JPT][hapmap]
rs3097714	0.88[JPT][hapmap]
rs3099946	0.83[AFR][1000 genomes]
rs3099955	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3099958	0.87[YRI][hapmap];0.91[AFR][1000 genomes]
rs3099968	1.00[JPT][hapmap]
rs3099990	1.00[JPT][hapmap]
rs3099995	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3112159	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3112163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3112166	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3112175	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3112178	0.88[JPT][hapmap]
rs3112184	1.00[JPT][hapmap]
rs3112188	1.00[JPT][hapmap]
rs3112189	1.00[JPT][hapmap]
rs3112191	1.00[JPT][hapmap]
rs3112192	1.00[JPT][hapmap]
rs3112196	1.00[JPT][hapmap]
rs3134637	1.00[JPT][hapmap]
rs3923144	0.82[CHB][hapmap]
rs4641916	0.84[EUR][1000 genomes]
rs4670266	0.96[CEU][hapmap];0.92[CHB][hapmap];0.92[EUR][1000 genomes]
rs4670268	0.86[JPT][hapmap]
rs4670900	0.92[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs61736780	0.87[AFR][1000 genomes]
rs6710418	0.97[EUR][1000 genomes]
rs6717670	1.00[JPT][hapmap]
rs6734584	0.95[EUR][1000 genomes]
rs6736353	0.85[AFR][1000 genomes]
rs6738069	0.86[ASN][1000 genomes]
rs6738403	0.90[EUR][1000 genomes]
rs6741088	0.86[EUR][1000 genomes]
rs72797376	0.88[AFR][1000 genomes]
rs72797386	0.87[AFR][1000 genomes]
rs72797392	0.85[AFR][1000 genomes]
rs72797402	0.85[AFR][1000 genomes]
rs7598922	0.85[CEU][hapmap];0.88[EUR][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	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3100000	DHX57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:39038800-39102200	Weak transcription	Gastric	stomach
3	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
5	chr2:39072200-39095400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:39073000-39091200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:39078200-39091200	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:39079800-39091000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:39079800-39091000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr2:39079800-39091200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:39080000-39092000	Strong transcription	Primary T cells from cord blood	blood
12	chr2:39080000-39102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:39081200-39102200	Weak transcription	Right Ventricle	heart
14	chr2:39081200-39102200	Weak transcription	Spleen	Spleen
15	chr2:39081200-39102400	Weak transcription	Pancreas	Pancrea
16	chr2:39081600-39093400	Weak transcription	Aorta	Aorta
17	chr2:39086000-39094400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:39086400-39101800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:39086600-39091400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:39086800-39091200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:39087600-39095400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:39087800-39091000	Strong transcription	HSMM	muscle
23	chr2:39088200-39102000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:39089200-39101800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:39089200-39101800	Weak transcription	Fetal Heart	heart
26	chr2:39089400-39093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:39089400-39093200	Weak transcription	NHEK	skin
28	chr2:39089400-39094000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:39089400-39094200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:39089400-39094600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:39089400-39095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:39089400-39101200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:39089400-39102000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:39089400-39102200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:39089400-39102200	Weak transcription	Ovary	ovary
36	chr2:39089400-39102200	Weak transcription	Small Intestine	intestine
37	chr2:39089600-39092400	Weak transcription	Psoas Muscle	Psoas
38	chr2:39089600-39093200	Weak transcription	NH-A	brain
39	chr2:39089600-39093400	Weak transcription	Fetal Brain Male	brain
40	chr2:39089600-39093800	Weak transcription	Fetal Stomach	stomach
41	chr2:39089600-39094000	Weak transcription	Thymus	Thymus
42	chr2:39089600-39094000	Weak transcription	Hela-S3	cervix
43	chr2:39089600-39094600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:39089600-39101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:39089600-39102000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:39089600-39102000	Weak transcription	NHLF	lung
47	chr2:39089600-39102400	Weak transcription	Lung	lung
48	chr2:39089800-39097200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:39089800-39101800	Weak transcription	Brain Substantia Nigra	brain
50	chr2:39090000-39093400	Weak transcription	Duodenum Mucosa	Duodenum

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