Variant report

Variant	rs9636439
Chromosome Location	chr2:55836366-55836367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55452223..55454388-chr2:55835681..55838374,2	K562	blood:
2	chr2:55820891..55824510-chr2:55834569..55837738,3	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10195281	0.81[AFR][1000 genomes]
rs10200159	0.88[AFR][1000 genomes]
rs10203953	0.80[AFR][1000 genomes]
rs10208774	0.83[YRI][hapmap]
rs10221888	0.90[YRI][hapmap]
rs1037508	0.90[ASN][1000 genomes]
rs10427222	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1045910	0.82[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10496044	0.93[YRI][hapmap]
rs11890141	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11900763	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12463766	0.89[ASN][1000 genomes]
rs12615063	0.83[YRI][hapmap]
rs12616502	0.86[YRI][hapmap]
rs12619756	0.83[ASN][1000 genomes]
rs12989898	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13016772	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13028892	0.94[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs13382187	0.93[YRI][hapmap]
rs13383352	0.93[YRI][hapmap]
rs13384322	0.83[YRI][hapmap]
rs13403782	0.84[ASN][1000 genomes]
rs13407344	0.93[YRI][hapmap]
rs1373228	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1563201	0.82[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs17047094	0.86[YRI][hapmap]
rs17047119	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs1975486	0.91[JPT][hapmap]
rs2168097	0.81[ASN][1000 genomes]
rs2586946	0.88[ASN][1000 genomes]
rs2586948	0.87[ASN][1000 genomes]
rs2586949	0.87[JPT][hapmap]
rs2586965	0.80[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2627758	0.87[ASN][1000 genomes]
rs2627763	0.83[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2627778	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2627783	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748945	0.82[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap];0.94[ASN][1000 genomes]
rs3748955	0.84[AFR][1000 genomes]
rs3816489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4233962	0.90[ASN][1000 genomes]
rs4671248	0.94[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs4671250	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62165178	0.90[ASN][1000 genomes]
rs6545503	0.90[JPT][hapmap]
rs6545505	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6545507	0.82[AFR][1000 genomes]
rs6545508	0.82[ASW][hapmap];0.87[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6545510	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs6545513	0.93[YRI][hapmap]
rs6712314	0.88[AFR][1000 genomes]
rs6716100	0.91[JPT][hapmap];0.93[YRI][hapmap]
rs6717574	0.86[YRI][hapmap]
rs6731927	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6736996	0.82[AFR][1000 genomes]
rs6745430	0.87[AFR][1000 genomes]
rs6745650	0.85[YRI][hapmap]
rs6760959	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs706549	0.84[CHD][hapmap]
rs706551	0.82[CHD][hapmap]
rs730884	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736345	0.85[YRI][hapmap];0.90[AFR][1000 genomes]
rs744514	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7558127	0.89[YRI][hapmap]
rs7571482	0.87[ASN][1000 genomes]
rs7574398	0.81[AFR][1000 genomes]
rs7574409	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7585484	0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7586124	0.82[ASW][hapmap];0.90[YRI][hapmap]
rs7594497	0.93[YRI][hapmap]
rs7605486	0.82[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7605504	0.82[ASN][1000 genomes]
rs782574	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs782583	0.82[CHD][hapmap]
rs782589	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs782591	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs782593	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs782597	0.81[ASN][1000 genomes]
rs782598	0.88[ASN][1000 genomes]
rs782603	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs782612	0.87[ASN][1000 genomes]
rs782620	0.86[CHD][hapmap]
rs782636	0.82[CHD][hapmap]
rs782648	0.84[ASN][1000 genomes]
rs782651	0.84[ASN][1000 genomes]
rs9309267	0.85[LWK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 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	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
3	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:55803000-55838800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:55824400-55837400	Weak transcription	Fetal Kidney	kidney
6	chr2:55826000-55839200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:55826000-55841600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:55826200-55842600	Weak transcription	Right Ventricle	heart
9	chr2:55826200-55843000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:55828200-55843600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:55828400-55838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:55829800-55838400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:55829800-55838400	Weak transcription	HMEC	breast
14	chr2:55829800-55838800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:55829800-55842800	Weak transcription	Colonic Mucosa	Colon
16	chr2:55830000-55838000	Weak transcription	Brain Germinal Matrix	brain
17	chr2:55830000-55838200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:55830000-55838600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:55830200-55837600	Weak transcription	NHEK	skin
20	chr2:55830200-55838000	Weak transcription	Adipose Nuclei	Adipose
21	chr2:55830200-55838200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:55830400-55836400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:55830400-55837400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:55830400-55837400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:55830400-55837400	Weak transcription	Fetal Lung	lung
26	chr2:55830400-55837400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:55830400-55837600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:55830400-55838000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:55830400-55838000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:55830400-55838000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:55830400-55838000	Weak transcription	Esophagus	oesophagus
32	chr2:55830400-55838000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:55830400-55838200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:55830400-55838200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:55830400-55838200	Weak transcription	Thymus	Thymus
36	chr2:55830400-55838400	Weak transcription	Brain Anterior Caudate	brain
37	chr2:55830400-55838400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:55830400-55838600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:55830400-55838800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:55830400-55838800	Weak transcription	Spleen	Spleen
41	chr2:55830400-55841000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:55830400-55842800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:55830400-55843600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:55830400-55843600	Weak transcription	Aorta	Aorta
45	chr2:55830600-55837600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:55830600-55838000	Weak transcription	HUVEC	blood vessel
47	chr2:55830600-55838200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:55830600-55838400	Weak transcription	Dnd41	blood
49	chr2:55830600-55838800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:55830800-55838200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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