Variant report

Variant	rs3102438
Chromosome Location	chr4:143201904-143201905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10029437	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1219266	1.00[CEU][hapmap]
rs1219268	1.00[CEU][hapmap]
rs1219269	1.00[CEU][hapmap]
rs1219270	1.00[CEU][hapmap]
rs13120882	0.83[YRI][hapmap]
rs1390994	1.00[CEU][hapmap]
rs1497139	1.00[CEU][hapmap]
rs1532450	1.00[CEU][hapmap]
rs1907109	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1907113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1907117	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907135	1.00[CEU][hapmap]
rs1907137	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1948323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2130685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2172023	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627812	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627816	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2627817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627834	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627835	0.88[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2627836	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636635	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2636637	0.81[CEU][hapmap]
rs2636641	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636642	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636643	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636647	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636652	0.89[YRI][hapmap];0.88[AMR][1000 genomes]
rs2636655	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636656	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636657	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636660	1.00[CEU][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636679	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2636685	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3102436	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3102437	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3102439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3102443	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3102444	0.95[EUR][1000 genomes]
rs3102446	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113511	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113515	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3113522	0.88[CEU][hapmap]
rs336384	1.00[CEU][hapmap]
rs336394	0.81[CEU][hapmap]
rs336400	0.83[CEU][hapmap]
rs336402	0.81[CEU][hapmap]
rs336405	0.83[CEU][hapmap]
rs336406	0.81[CEU][hapmap]
rs34648309	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830098	chr4:143050143-143234384	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv595604	chr4:143077401-143228914	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143183000-143204800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:143187400-143203800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:143187400-143218600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:143192000-143210600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:143192000-143219400	Weak transcription	Dnd41	blood
6	chr4:143192200-143203800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr4:143192200-143206000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr4:143196000-143225200	Weak transcription	NHDF-Ad	bronchial
9	chr4:143196200-143203600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:143196800-143203200	Weak transcription	A549	lung
11	chr4:143197400-143202200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:143197600-143203800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:143199400-143230800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:143199600-143203400	Weak transcription	Aorta	Aorta
15	chr4:143199600-143204200	Weak transcription	Osteobl	bone
16	chr4:143199800-143203200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:143199800-143203800	Weak transcription	HSMM	muscle
18	chr4:143199800-143204200	Weak transcription	Primary T cells from cord blood	blood
19	chr4:143200000-143215000	Weak transcription	HSMMtube	muscle
20	chr4:143200000-143240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:143200200-143202000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:143200200-143203000	Weak transcription	HMEC	breast
23	chr4:143200200-143203200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:143200200-143203200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:143200200-143203200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:143200200-143210600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:143200600-143203000	Weak transcription	NHEK	skin
28	chr4:143201000-143202000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:143201000-143203200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:143201400-143202800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:143201400-143204200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr4:143201600-143203800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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