Variant report

Variant	rs3109954
Chromosome Location	chr4:107258227-107258228
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	chr4:107238261..107242846-chr4:107256432..107259782,4	K562	blood:

Variant related genes	Relation type
ENSG00000145348	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10004034	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10017707	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10025668	0.80[ASN][1000 genomes]
rs10516530	0.93[ASN][1000 genomes]
rs10516531	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097923	0.95[ASN][1000 genomes]
rs1134648	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs11938792	0.95[ASN][1000 genomes]
rs12512475	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17036581	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691805	1.00[ASN][1000 genomes]
rs2691806	1.00[ASN][1000 genomes]
rs2728176	1.00[ASN][1000 genomes]
rs2728177	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28418378	0.80[ASN][1000 genomes]
rs2949626	0.99[ASN][1000 genomes]
rs2949649	0.94[ASN][1000 genomes]
rs2949651	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3018057	0.93[ASN][1000 genomes]
rs3018059	0.99[ASN][1000 genomes]
rs3018067	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3109950	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3109951	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3109952	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109956	1.00[ASN][1000 genomes]
rs3109959	0.87[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs3113246	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113251	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133167	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3133172	1.00[ASN][1000 genomes]
rs3133173	0.86[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34305991	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34923623	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4415033	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4441824	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4560491	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4582218	0.94[ASN][1000 genomes]
rs57983950	0.94[ASN][1000 genomes]
rs6533241	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533244	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6848855	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7442226	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7669347	0.81[ASN][1000 genomes]
rs7677394	0.87[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7680756	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7694217	0.87[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[ASN][1000 genomes]
rs9991203	0.80[ASN][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	nsv830029	chr4:107203096-107353483	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 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	chr4:107238600-107258400	Weak transcription	Spleen	Spleen
2	chr4:107238600-107258600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:107238600-107259600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:107238600-107259600	Weak transcription	Pancreas	Pancrea
5	chr4:107238800-107259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:107239000-107259200	Weak transcription	Fetal Brain Male	brain
7	chr4:107239200-107258400	Weak transcription	Aorta	Aorta
8	chr4:107239200-107259400	Weak transcription	Psoas Muscle	Psoas
9	chr4:107242200-107258600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:107242800-107258400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:107242800-107259400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:107243400-107271400	Weak transcription	Right Ventricle	heart
13	chr4:107243800-107259600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:107244200-107258400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:107245600-107259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr4:107245800-107258400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:107245800-107259000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:107245800-107261800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr4:107245800-107262200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr4:107245800-107263000	Strong transcription	Dnd41	blood
21	chr4:107246000-107258400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:107246000-107262000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:107246200-107262000	Strong transcription	NH-A	brain
24	chr4:107246400-107259400	Strong transcription	Placenta	Placenta
25	chr4:107246800-107260200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:107246800-107260800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:107247000-107258600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:107247000-107258800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:107247000-107259600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:107247000-107260600	Strong transcription	Adipose Nuclei	Adipose
31	chr4:107247000-107261200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:107247000-107261800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr4:107247000-107262000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr4:107247000-107262200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr4:107247000-107263000	Strong transcription	Fetal Intestine Large	intestine
36	chr4:107247000-107263600	Strong transcription	Fetal Thymus	thymus
37	chr4:107247000-107271400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:107247200-107260400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:107247400-107258600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:107247400-107260600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:107247400-107262600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:107247600-107258800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:107247600-107262400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:107247600-107263600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:107247800-107260600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:107248000-107259800	Strong transcription	Colon Smooth Muscle	Colon
47	chr4:107248000-107262000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:107248400-107258800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr4:107248600-107261800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:107248800-107260800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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