Variant report

Variant	rs12563515
Chromosome Location	chr1:85739861-85739862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:85738169-85740047	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:85739539-85742754	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:85738277-85742976	IMR90	lung:	n/a	n/a
4	CHD1	chr1:85739832-85743054	IMR90	lung:	n/a	n/a
5	POLR2A	chr1:85738320-85740116	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:85739753..85743262-chr1:86045535..86049012,3	K562	blood:
2	chr1:85665631..85669772-chr1:85739485..85744059,5	K562	blood:
3	chr1:85731137..85733599-chr1:85736126..85739884,4	MCF-7	breast:
4	chr1:85723140..85725993-chr1:85738626..85740807,2	MCF-7	breast:
5	chr1:85723214..85729954-chr1:85738689..85743771,11	K562	blood:
6	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000223653	TF binding region
ENSG00000162642	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000097096	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1060843	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11161564	0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11161581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161583	0.96[ASN][1000 genomes]
rs11161587	0.85[YRI][hapmap]
rs12065528	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12066982	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12068389	0.93[ASN][1000 genomes]
rs12068788	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12084232	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12086970	0.93[ASN][1000 genomes]
rs12087340	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs12098111	0.85[YRI][hapmap]
rs12098220	0.85[YRI][hapmap]
rs12726649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743302	0.96[ASN][1000 genomes]
rs12744565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746169	0.92[ASN][1000 genomes]
rs17124345	0.93[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs35486093	0.96[ASN][1000 genomes]
rs35783363	0.93[ASN][1000 genomes]
rs35798604	0.96[ASN][1000 genomes]
rs36116171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074156	0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs4258258	0.96[ASN][1000 genomes]
rs6693229	0.93[ASN][1000 genomes]
rs9887811	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9887812	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9887879	0.90[AFR][1000 genomes];0.96[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85725400-85741000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:85726000-85741000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:85726000-85741400	Weak transcription	Gastric	stomach
4	chr1:85727200-85741400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:85732600-85741000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:85734800-85740200	Weak transcription	Right Atrium	heart
7	chr1:85735000-85741400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:85735000-85741400	Weak transcription	Pancreas	Pancrea
9	chr1:85735400-85740600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:85735600-85740000	Weak transcription	Brain Angular Gyrus	brain
11	chr1:85735600-85740000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:85735600-85740400	Weak transcription	A549	lung
13	chr1:85735600-85741400	Weak transcription	Lung	lung
14	chr1:85735800-85740000	Weak transcription	Fetal Brain Male	brain
15	chr1:85735800-85740200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:85735800-85740600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:85736200-85740000	Weak transcription	Brain Anterior Caudate	brain
18	chr1:85736200-85740200	Weak transcription	Ovary	ovary
19	chr1:85736200-85740200	Weak transcription	Thymus	Thymus
20	chr1:85736200-85740600	Weak transcription	Esophagus	oesophagus
21	chr1:85736400-85740000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:85736400-85740200	Weak transcription	Fetal Kidney	kidney
23	chr1:85736400-85740200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:85736800-85740400	Weak transcription	Brain Substantia Nigra	brain
25	chr1:85736800-85740600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:85736800-85741000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:85737000-85740000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:85737000-85740200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:85737000-85740200	Weak transcription	Fetal Lung	lung
30	chr1:85737000-85740200	Weak transcription	Fetal Stomach	stomach
31	chr1:85737000-85741000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:85737200-85740000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:85737200-85740000	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:85737400-85740600	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr1:85737600-85740800	Weak transcription	Left Ventricle	heart
36	chr1:85737800-85740000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:85737800-85740000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:85737800-85741200	Weak transcription	Placenta	Placenta
39	chr1:85738000-85740200	Weak transcription	Fetal Thymus	thymus
40	chr1:85738200-85740400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr1:85738200-85740600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:85738400-85740200	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:85738400-85740400	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr1:85738600-85740000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
45	chr1:85738600-85740000	Active TSS	GM12878-XiMat	blood
46	chr1:85738600-85740800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:85738600-85740800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr1:85738800-85740200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:85738800-85740600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:85738800-85740600	Enhancers	Adipose Nuclei	Adipose

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