Variant report

Variant	rs1864828
Chromosome Location	chr2:38824781-38824782
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:38823056-38824832	K562	blood:	n/a	n/a
2	POLR2A	chr2:38821640-38832164	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38823060..38827854-chr2:38827983..38831423,11	MCF-7	breast:
2	chr2:38824718..38826820-chr2:38951264..38953232,2	K562	blood:
3	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
4	chr2:38823156..38825243-chr2:38925773..38928004,2	K562	blood:
5	chr2:38822893..38825624-chr2:38929270..38931305,2	K562	blood:
6	chr2:38823810..38825373-chr2:38867072..38871026,3	K562	blood:
7	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
8	chr2:38824026..38825901-chr2:38962946..38965190,2	K562	blood:
9	chr2:38824210..38826669-chr2:38912161..38913673,2	MCF-7	breast:
10	chr2:38820462..38822126-chr2:38823935..38825729,2	MCF-7	breast:
11	chr2:38823862..38826061-chr2:38919360..38922289,2	K562	blood:
12	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
13	chr2:38823625..38826319-chr2:38903588..38906507,3	K562	blood:
14	chr2:38824770..38827325-chr2:38977013..38980268,3	MCF-7	breast:
15	chr2:38821957..38830238-chr2:38965333..38974515,17	K562	blood:
16	chr2:38823851..38826080-chr2:38908814..38911340,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235586	TF binding region
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000235586	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10495880	0.89[JPT][hapmap]
rs12105827	0.89[EUR][1000 genomes]
rs12987111	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12990659	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12995222	0.84[ASN][1000 genomes]
rs12996029	1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13011896	0.90[AFR][1000 genomes]
rs1540436	1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17421378	0.90[JPT][hapmap]
rs17421399	1.00[CEU][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17421503	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs17421743	0.80[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17493321	0.95[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs17493370	0.90[JPT][hapmap]
rs17493419	0.90[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs17493538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17493573	1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17493594	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864829	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1864830	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3213851	0.94[ASN][1000 genomes]
rs34218951	0.88[EUR][1000 genomes]
rs34462852	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35679136	0.85[AFR][1000 genomes]
rs35734673	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35933789	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4268910	1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56217714	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6544170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6721860	0.81[EUR][1000 genomes]
rs6731029	0.89[JPT][hapmap]
rs6733848	0.89[JPT][hapmap]
rs6745023	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6757844	0.85[EUR][1000 genomes]
rs68109027	0.80[AFR][1000 genomes]
rs72905846	0.80[AFR][1000 genomes]
rs72905865	0.80[AFR][1000 genomes]
rs72907903	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7573095	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7574556	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs891705	0.89[JPT][hapmap]
rs934394	0.89[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs934395	0.90[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
2	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
5	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
6	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:38799800-38827800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:38805200-38826400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:38808800-38825200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:38808800-38825400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:38808800-38827000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:38808800-38827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:38808800-38827400	Weak transcription	Pancreas	Pancrea
14	chr2:38809000-38825600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:38809400-38825800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:38809600-38827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:38810000-38827600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:38813200-38826000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:38813400-38827000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:38813800-38825400	Weak transcription	Primary T cells from cord blood	blood
21	chr2:38814400-38825200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:38814400-38825600	Weak transcription	HUVEC	blood vessel
23	chr2:38815200-38825200	Weak transcription	Gastric	stomach
24	chr2:38815200-38825400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:38815200-38825800	Weak transcription	Fetal Brain Male	brain
26	chr2:38815400-38825400	Weak transcription	Fetal Kidney	kidney
27	chr2:38818000-38825400	Weak transcription	Brain Substantia Nigra	brain
28	chr2:38818200-38825200	Weak transcription	Brain Germinal Matrix	brain
29	chr2:38818200-38825400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:38818400-38827600	Weak transcription	Placenta	Placenta
31	chr2:38818800-38825200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:38818800-38825400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:38818800-38825400	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:38818800-38825600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:38818800-38825600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:38818800-38825600	Weak transcription	HSMM	muscle
37	chr2:38819000-38825200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:38819600-38827400	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr2:38820200-38825600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:38820200-38827800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr2:38820400-38825200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:38820400-38825400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:38820600-38825200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:38820600-38825400	Weak transcription	NH-A	brain
45	chr2:38820800-38825200	Weak transcription	NHDF-Ad	bronchial
46	chr2:38820800-38825200	Weak transcription	Osteobl	bone
47	chr2:38820800-38825400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:38820800-38825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:38820800-38825400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr2:38821000-38825200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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