Variant report

Variant	rs235507
Chromosome Location	chr1:171542886-171542887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171501615..171504205-chr1:171542764..171544270,2	K562	blood:
2	chr1:171529487..171532433-chr1:171541156..171543384,2	MCF-7	breast:
3	chr1:171542641..171545626-chr1:171731101..171734009,2	K562	blood:
4	chr1:171533246..171538102-chr1:171538740..171543133,5	K562	blood:

Variant related genes	Relation type
ENSG00000236741	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1055417	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10913167	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12129856	0.84[EUR][1000 genomes]
rs12131694	0.83[EUR][1000 genomes]
rs12136576	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12137832	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12139715	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12142594	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12145045	0.90[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	0.94[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	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs190198	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294292	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2294293	0.94[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235495	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235498	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235502	1.00[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235892	0.87[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	0.87[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	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235900	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235901	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235902	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235903	0.87[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235911	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235912	1.00[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[AFR][1000 genomes];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	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs74122850	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7534464	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7534557	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7538745	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][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	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
4	nsv465639	chr1:171459507-171545051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv548190	chr1:171459507-171545051	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr1:171524200-171549600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:171524200-171562800	Strong transcription	Liver	Liver
9	chr1:171524200-171564400	Strong transcription	Adipose Nuclei	Adipose
10	chr1:171524400-171549000	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:171524400-171549000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:171524400-171553000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:171524400-171558200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:171524400-171563600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:171524400-171564400	Strong transcription	Fetal Thymus	thymus
16	chr1:171524400-171564600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:171524400-171566400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:171524600-171558600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:171525200-171555200	Strong transcription	Primary B cells from cord blood	blood
20	chr1:171525200-171564000	Strong transcription	HUVEC	blood vessel
21	chr1:171525400-171544400	Weak transcription	Stomach Mucosa	stomach
22	chr1:171525400-171563600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:171525600-171549600	Strong transcription	NHDF-Ad	bronchial
24	chr1:171525600-171562200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:171525600-171562800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:171525600-171563800	Strong transcription	HSMM	muscle
27	chr1:171525800-171552000	Strong transcription	Hela-S3	cervix
28	chr1:171525800-171564400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:171526200-171561800	Strong transcription	K562	blood
30	chr1:171526800-171562800	Strong transcription	Dnd41	blood
31	chr1:171527200-171560600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:171527200-171562800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:171528200-171563800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:171528400-171545800	Weak transcription	Pancreas	Pancrea
35	chr1:171528400-171547400	Weak transcription	Fetal Brain Male	brain
36	chr1:171528400-171564600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:171528600-171558200	Strong transcription	GM12878-XiMat	blood
38	chr1:171528600-171564400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:171529200-171546400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:171529200-171563400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:171529400-171564800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:171529600-171554400	Strong transcription	Primary hematopoietic stem cells	blood
43	chr1:171529600-171563600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:171529600-171566200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:171530600-171546600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:171530600-171549400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:171530800-171547400	Weak transcription	Small Intestine	intestine
48	chr1:171531200-171547200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:171531200-171563600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:171532200-171543600	Weak transcription	Brain Substantia Nigra	brain

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