Variant report

Variant	rs12059944
Chromosome Location	chr1:169449870-169449871
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169336376..169338825-chr1:169448253..169450809,2	K562	blood:
2	chr1:169433035..169435323-chr1:169448952..169451529,2	K562	blood:

Variant related genes	Relation type
ENSG00000143156	Chromatin interaction
ENSG00000117475	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10047168	0.85[ASN][1000 genomes]
rs10800430	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs10800436	0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10800443	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10800445	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10919151	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10919152	0.87[ASN][1000 genomes]
rs10919156	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10919157	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10919159	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11487548	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11810815	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12061080	0.87[ASN][1000 genomes]
rs12065030	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12071630	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12073439	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12074966	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12081030	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12091133	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12091844	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12092506	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12092952	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12094791	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12097682	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12561922	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12565852	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2038024	0.80[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2275300	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2280257	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2901092	0.80[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3737683	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3765227	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766088	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs41272453	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7522245	0.86[CHB][hapmap]
rs9628661	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription 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 lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169430000-169450000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:169430000-169452000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr1:169430000-169452000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:169430000-169452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:169430000-169452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:169430000-169452800	Weak transcription	Brain Germinal Matrix	brain
7	chr1:169430000-169452800	Weak transcription	HMEC	breast
8	chr1:169430000-169452800	Weak transcription	NHDF-Ad	bronchial
9	chr1:169430000-169452800	Weak transcription	NHEK	skin
10	chr1:169430000-169453400	Weak transcription	Colonic Mucosa	Colon
11	chr1:169430000-169453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:169430000-169454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:169430000-169454400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:169430000-169454400	Weak transcription	Spleen	Spleen
15	chr1:169430200-169450600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:169430200-169451800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:169430200-169452600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:169430200-169452600	Weak transcription	NH-A	brain
19	chr1:169430200-169453200	Weak transcription	Esophagus	oesophagus
20	chr1:169430600-169452800	Weak transcription	Small Intestine	intestine
21	chr1:169431200-169452000	Weak transcription	GM12878-XiMat	blood
22	chr1:169434600-169452600	Weak transcription	Primary B cells from cord blood	blood
23	chr1:169435200-169452800	Weak transcription	Fetal Kidney	kidney
24	chr1:169437400-169450600	Weak transcription	Brain Angular Gyrus	brain
25	chr1:169437400-169452600	Weak transcription	HSMMtube	muscle
26	chr1:169437400-169452600	Weak transcription	Osteobl	bone
27	chr1:169437400-169452800	Weak transcription	Aorta	Aorta
28	chr1:169437400-169452800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:169437800-169452600	Weak transcription	Fetal Brain Female	brain
30	chr1:169438600-169452200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:169438600-169453200	Weak transcription	Fetal Lung	lung
32	chr1:169438800-169452600	Weak transcription	HSMM	muscle
33	chr1:169439200-169452000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:169439600-169452600	Weak transcription	Primary T cells from cord blood	blood
35	chr1:169443000-169452800	Weak transcription	A549	lung
36	chr1:169443800-169452800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:169444200-169451800	Weak transcription	Brain Substantia Nigra	brain
38	chr1:169444200-169454000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:169444600-169452600	Weak transcription	Stomach Mucosa	stomach
40	chr1:169444600-169452800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:169446600-169453000	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:169446800-169451000	Weak transcription	Left Ventricle	heart
43	chr1:169446800-169452000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:169446800-169452000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:169446800-169452000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:169446800-169452000	Weak transcription	Dnd41	blood
47	chr1:169446800-169452400	Weak transcription	Brain Anterior Caudate	brain
48	chr1:169446800-169452600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:169446800-169452600	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:169446800-169452600	Weak transcription	Placenta	Placenta

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