Variant report

Variant	rs17421399
Chromosome Location	chr2:38769087-38769088
allele	A/C
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:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38766012..38769150-chr2:38977122..38980582,4	K562	blood:
2	chr2:38742072..38744914-chr2:38766653..38769930,3	K562	blood:
3	chr2:38751112..38753312-chr2:38768692..38771301,2	K562	blood:
4	chr2:38767755..38769303-chr2:38769457..38771424,2	K562	blood:
5	chr2:38756770..38758760-chr2:38767027..38769567,2	K562	blood:
6	chr2:38767365..38769438-chr2:38773461..38775183,2	MCF-7	breast:
7	chr2:38768041..38770034-chr2:38779562..38781817,2	K562	blood:
8	chr2:38751052..38753238-chr2:38767165..38769647,2	MCF-7	breast:
9	chr2:38765872..38769105-chr2:38828205..38830691,3	MCF-7	breast:
10	chr2:38761874..38764220-chr2:38767689..38769957,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HNRPLL-1	chr2:38768888-38769283	XLOC_002054

No data

Variant related genes	Relation type
ENSG00000231367	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000271443	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12105827	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12993657	0.90[ASN][1000 genomes]
rs12996029	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs13003268	0.89[ASN][1000 genomes]
rs13008970	0.91[ASN][1000 genomes]
rs13011825	0.90[ASN][1000 genomes]
rs13017981	0.91[ASN][1000 genomes]
rs1540436	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17421378	1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17421503	0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17421743	0.80[CEU][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap]
rs17493321	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17493363	0.82[JPT][hapmap]
rs17493370	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs17493419	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17493538	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs17493573	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs17493594	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17603796	0.91[JPT][hapmap]
rs1864828	1.00[CEU][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34171322	0.83[ASN][1000 genomes]
rs34218951	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34311924	0.90[ASN][1000 genomes]
rs34355269	0.87[ASN][1000 genomes]
rs34655983	0.93[ASN][1000 genomes]
rs35066504	0.90[ASN][1000 genomes]
rs35120096	0.89[ASN][1000 genomes]
rs35275207	0.89[ASN][1000 genomes]
rs35299812	0.82[ASN][1000 genomes]
rs35704960	0.93[ASN][1000 genomes]
rs35789272	0.93[ASN][1000 genomes]
rs35803605	0.83[ASN][1000 genomes]
rs3731843	0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs4268910	0.90[JPT][hapmap];0.93[YRI][hapmap]
rs56217714	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56311849	0.82[EUR][1000 genomes]
rs6544170	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6745023	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72795132	0.90[ASN][1000 genomes]
rs7571463	0.85[EUR][1000 genomes]
rs7573095	0.89[EUR][1000 genomes]
rs7574556	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7584009	0.83[ASN][1000 genomes]
rs7592090	0.90[ASN][1000 genomes]
rs7603200	0.89[ASN][1000 genomes]
rs7606253	0.90[ASN][1000 genomes]
rs7606376	0.90[ASN][1000 genomes]
rs934394	1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs934395	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]

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	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	esv1796304	chr2:38766721-38790750	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38770200	Weak transcription	HSMMtube	muscle
2	chr2:38763600-38771000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:38763800-38769400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:38763800-38769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:38763800-38778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:38764200-38769600	Weak transcription	A549	lung
8	chr2:38767200-38769400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:38767400-38770000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:38767400-38773400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:38767600-38769200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:38767600-38769200	Enhancers	Colon Smooth Muscle	Colon
13	chr2:38767600-38769800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:38767600-38770400	Enhancers	Fetal Intestine Large	intestine
15	chr2:38767800-38771200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr2:38768000-38769200	Enhancers	Stomach Smooth Muscle	stomach
17	chr2:38768200-38769800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:38768200-38770200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr2:38768200-38770200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr2:38768200-38770400	Enhancers	H9 Cell Line	embryonic stem cell
21	chr2:38768200-38770600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
23	chr2:38768400-38769200	Enhancers	Liver	Liver
24	chr2:38768400-38770400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr2:38768400-38771200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr2:38768400-38787800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:38768400-38788000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:38768400-38791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:38768600-38769200	Enhancers	Brain Anterior Caudate	brain
30	chr2:38768600-38769600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:38768600-38769600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:38768600-38769800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:38768600-38769800	Weak transcription	Fetal Intestine Small	intestine
34	chr2:38768800-38769600	Enhancers	HUVEC	blood vessel
35	chr2:38768800-38769600	Enhancers	NH-A	brain
36	chr2:38768800-38769800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:38768800-38779000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:38769000-38769200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:38769000-38769200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:38769000-38769400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:38769000-38769800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr2:38769000-38769800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:38769000-38769800	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr2:38769000-38769800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:38769000-38769800	Enhancers	Hela-S3	cervix
46	chr2:38769000-38769800	Enhancers	HepG2	liver
47	chr2:38769000-38770000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr2:38769000-38770000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr2:38769000-38770400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:38769000-38770400	Enhancers	Primary T cells from cord blood	blood

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