Variant report

Variant	rs236897
Chromosome Location	chr1:171673941-171673942
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	chr1:171642979..171645264-chr1:171671539..171674041,2	MCF-7	breast:
2	chr1:171673211..171675541-chr1:171709972..171711571,2	K562	blood:

Variant related genes	Relation type
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1045456	0.86[EUR][1000 genomes]
rs10489252	0.86[EUR][1000 genomes]
rs10913683	0.86[EUR][1000 genomes]
rs10913684	0.86[EUR][1000 genomes]
rs12091786	0.86[EUR][1000 genomes]
rs12565176	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12567851	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12730717	0.86[EUR][1000 genomes]
rs12742601	0.87[EUR][1000 genomes]
rs12753043	0.86[EUR][1000 genomes]
rs17596025	0.87[EUR][1000 genomes]
rs17596081	0.87[EUR][1000 genomes]
rs17649609	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17650310	0.86[EUR][1000 genomes]
rs17650340	0.86[EUR][1000 genomes]
rs1801898	0.86[EUR][1000 genomes]
rs2143369	0.86[EUR][1000 genomes]
rs2181216	0.87[EUR][1000 genomes]
rs2223602	0.87[EUR][1000 genomes]
rs2232807	0.85[EUR][1000 genomes]
rs2232813	0.86[EUR][1000 genomes]
rs2232819	0.87[EUR][1000 genomes]
rs2232824	0.86[EUR][1000 genomes]
rs236894	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs236898	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs236900	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34320898	0.87[EUR][1000 genomes]
rs34627492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35249022	0.85[EUR][1000 genomes]
rs35400839	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35631282	0.87[EUR][1000 genomes]
rs35674909	0.87[EUR][1000 genomes]
rs35882887	0.86[EUR][1000 genomes]
rs35930163	0.86[EUR][1000 genomes]
rs36080557	0.86[EUR][1000 genomes]
rs3891278	0.86[EUR][1000 genomes]
rs56365362	0.86[EUR][1000 genomes]
rs56377810	0.87[EUR][1000 genomes]
rs61807979	0.86[EUR][1000 genomes]
rs6656852	0.86[EUR][1000 genomes]
rs6674364	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6675708	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6681322	0.86[EUR][1000 genomes]
rs6689125	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6695933	0.87[EUR][1000 genomes]
rs7522582	0.86[EUR][1000 genomes]
rs7536142	0.86[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	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	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1800458	chr1:171667663-171701129	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs236897	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171664400-171685800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:171664600-171674400	Weak transcription	Primary T cells from cord blood	blood
3	chr1:171664800-171684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
5	chr1:171665400-171674600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:171666000-171674200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:171666000-171676000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:171666000-171676600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:171666000-171685000	Weak transcription	Brain Germinal Matrix	brain
12	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
13	chr1:171666200-171676000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:171666200-171682600	Weak transcription	Lung	lung
15	chr1:171666200-171684600	Weak transcription	Fetal Stomach	stomach
16	chr1:171666200-171684800	Weak transcription	Thymus	Thymus
17	chr1:171666600-171676600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:171666600-171684800	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:171666600-171686200	Weak transcription	Gastric	stomach
20	chr1:171666800-171674200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:171666800-171674200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:171666800-171675600	Weak transcription	Colonic Mucosa	Colon
23	chr1:171666800-171679200	Weak transcription	NH-A	brain
24	chr1:171666800-171686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:171666800-171692000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:171666800-171692000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:171666800-171692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:171667000-171675800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:171667000-171676600	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:171667000-171676800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:171667000-171685000	Weak transcription	Osteobl	bone
33	chr1:171667000-171692000	Weak transcription	Fetal Brain Female	brain
34	chr1:171667000-171692200	Weak transcription	Brain Anterior Caudate	brain
35	chr1:171667600-171674400	Weak transcription	Placenta	Placenta
36	chr1:171667600-171676200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:171667600-171681200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:171667600-171692000	Weak transcription	Fetal Lung	lung
39	chr1:171667800-171676400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:171667800-171688400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:171667800-171688800	Weak transcription	Spleen	Spleen
42	chr1:171667800-171692000	Weak transcription	Fetal Thymus	thymus
43	chr1:171668000-171674400	Weak transcription	HSMMtube	muscle
44	chr1:171668000-171685800	Weak transcription	Esophagus	oesophagus
45	chr1:171668200-171680200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:171668400-171676600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:171668400-171677200	Strong transcription	NHDF-Ad	bronchial
48	chr1:171668600-171684800	Weak transcription	Fetal Kidney	kidney
49	chr1:171668600-171692400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:171668800-171674200	Weak transcription	Adipose Nuclei	Adipose

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