Variant report

Variant	rs10489894
Chromosome Location	chr1:173866024-173866025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173853219..173856006-chr1:173864250..173866339,2	K562	blood:
2	chr1:173834928..173838432-chr1:173865557..173868884,4	MCF-7	breast:
3	chr1:173859716..173863027-chr1:173865455..173870785,5	K562	blood:
4	chr1:173854070..173860394-chr1:173860539..173867294,11	MCF-7	breast:
5	chr1:173865468..173869830-chr1:173871500..173875883,4	MCF-7	breast:
6	chr1:173863088..173867176-chr1:173869417..173872260,5	MCF-7	breast:
7	chr1:173865064..173869391-chr1:173883979..173888192,4	MCF-7	breast:
8	chr1:173856030..173858273-chr1:173864244..173866649,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB37-3	chr1:173865073-173866531	NONHSAT007706

No data

Variant related genes	Relation type
ENSG00000117601	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1535527	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846439	1.00[YRI][hapmap]
rs16846529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17359906	0.96[ASN][1000 genomes]
rs1969757	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227607	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2227609	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2281486	1.00[YRI][hapmap]
rs2295957	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791020	1.00[YRI][hapmap]
rs55829688	0.81[AFR][1000 genomes]
rs56064477	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56288561	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56382804	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59675210	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61609614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827869	0.93[ASN][1000 genomes]
rs6667813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700754	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709385	0.86[ASN][1000 genomes]
rs72709390	0.86[ASN][1000 genomes]
rs72711419	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711423	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711425	0.93[ASN][1000 genomes]
rs7525115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660881	0.81[AFR][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active 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	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
5	nsv8535	chr1:173863986-173866800	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173841000-173868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:173855400-173868000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:173855600-173866800	Weak transcription	Pancreas	Pancrea
4	chr1:173855600-173875400	Weak transcription	NH-A	brain
5	chr1:173855800-173873000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:173855800-173880400	Weak transcription	Thymus	Thymus
7	chr1:173856000-173868400	Weak transcription	Hela-S3	cervix
8	chr1:173856000-173868600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:173856000-173869400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:173856000-173869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:173856000-173872600	Weak transcription	Fetal Thymus	thymus
12	chr1:173856000-173883000	Weak transcription	Right Ventricle	heart
13	chr1:173856200-173866200	Weak transcription	GM12878-XiMat	blood
14	chr1:173856200-173867800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:173856200-173868800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:173856200-173868800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:173856200-173869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:173856200-173872800	Weak transcription	Ovary	ovary
19	chr1:173856200-173875400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:173856200-173878400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:173856200-173880400	Weak transcription	Psoas Muscle	Psoas
22	chr1:173856400-173867200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:173856400-173868200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:173856400-173873800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:173856400-173876000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:173856400-173880000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:173856600-173868000	Weak transcription	NHDF-Ad	bronchial
28	chr1:173856600-173881200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
30	chr1:173856800-173868800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:173857000-173866200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:173857000-173883800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:173857200-173866200	Weak transcription	Brain Anterior Caudate	brain
34	chr1:173857400-173866600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:173857400-173869000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:173857400-173869400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:173857400-173880400	Weak transcription	Fetal Brain Female	brain
38	chr1:173857400-173881800	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:173857400-173884400	Weak transcription	HepG2	liver
40	chr1:173857400-173885800	Weak transcription	Fetal Intestine Large	intestine
41	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
42	chr1:173857600-173868400	Weak transcription	Osteobl	bone
43	chr1:173857600-173870000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:173857600-173872600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
46	chr1:173858400-173878600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:173858600-173881400	Weak transcription	Primary B cells from cord blood	blood
48	chr1:173858600-173886800	Weak transcription	Placenta	Placenta
49	chr1:173858800-173871400	Weak transcription	HSMM	muscle
50	chr1:173858800-173872200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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