Variant report

Variant	rs235498
Chromosome Location	chr1:171555242-171555243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1055417	0.88[EUR][1000 genomes]
rs10913167	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12129856	0.84[EUR][1000 genomes]
rs12131694	0.83[EUR][1000 genomes]
rs12136576	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12137832	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12139715	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12142594	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12145045	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12146022	0.84[EUR][1000 genomes]
rs12733939	0.83[EUR][1000 genomes]
rs12734261	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12759907	0.83[EUR][1000 genomes]
rs171005	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183533	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs190198	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294292	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2294293	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs235471	0.80[ASN][1000 genomes]
rs235472	0.80[ASN][1000 genomes]
rs235477	0.83[AMR][1000 genomes]
rs235488	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235495	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235502	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235507	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235865	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235886	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235892	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235893	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235895	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235897	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs235898	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235899	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235900	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235901	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235902	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235903	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235904	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235910	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235911	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235912	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661007	1.00[ASN][1000 genomes]
rs46407	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536753	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559739	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56207586	0.83[EUR][1000 genomes]
rs591286	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631259	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67133611	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71637410	0.83[EUR][1000 genomes]
rs71637418	0.80[ASN][1000 genomes]
rs71637419	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs74122850	0.83[EUR][1000 genomes]
rs7534464	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7534557	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7538745	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171521600-171563800	Strong transcription	Rectal Mucosa Donor 29	rectum
2	chr1:171521800-171562800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:171522600-171564000	Strong transcription	Duodenum Mucosa	Duodenum
4	chr1:171522800-171564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:171522800-171564200	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr1:171522800-171564400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:171524200-171562800	Strong transcription	Liver	Liver
8	chr1:171524200-171564400	Strong transcription	Adipose Nuclei	Adipose
9	chr1:171524400-171558200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:171524400-171563600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:171524400-171564400	Strong transcription	Fetal Thymus	thymus
12	chr1:171524400-171564600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:171524400-171566400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:171524600-171558600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:171525200-171564000	Strong transcription	HUVEC	blood vessel
16	chr1:171525400-171563600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:171525600-171562200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:171525600-171562800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:171525600-171563800	Strong transcription	HSMM	muscle
20	chr1:171525800-171564400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:171526200-171561800	Strong transcription	K562	blood
22	chr1:171526800-171562800	Strong transcription	Dnd41	blood
23	chr1:171527200-171560600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:171527200-171562800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:171528200-171563800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:171528400-171564600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:171528600-171558200	Strong transcription	GM12878-XiMat	blood
28	chr1:171528600-171564400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:171529200-171563400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:171529400-171564800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:171529600-171563600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:171529600-171566200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:171531200-171563600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:171532600-171564200	Strong transcription	Placenta	Placenta
35	chr1:171533000-171564000	Strong transcription	Fetal Intestine Large	intestine
36	chr1:171533400-171562600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:171533600-171558200	Strong transcription	NH-A	brain
38	chr1:171539000-171565000	Strong transcription	Primary T cells from cord blood	blood
39	chr1:171539200-171562800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:171539600-171565200	Weak transcription	Fetal Heart	heart
41	chr1:171540000-171564000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:171540600-171563600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:171541600-171562200	Strong transcription	Fetal Kidney	kidney
44	chr1:171543200-171562200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:171543400-171562200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:171543400-171562800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:171543400-171563200	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr1:171543400-171563800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr1:171543600-171555400	Strong transcription	NHLF	lung
50	chr1:171543600-171558400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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