Variant report

Variant	rs6732743
Chromosome Location	chr2:38768464-38768465
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:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 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	chr2:38767755..38769303-chr2:38769457..38771424,2	K562	blood:
4	chr2:38756770..38758760-chr2:38767027..38769567,2	K562	blood:
5	chr2:38767365..38769438-chr2:38773461..38775183,2	MCF-7	breast:
6	chr2:38768041..38770034-chr2:38779562..38781817,2	K562	blood:
7	chr2:38751052..38753238-chr2:38767165..38769647,2	MCF-7	breast:
8	chr2:38765872..38769105-chr2:38828205..38830691,3	MCF-7	breast:
9	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	chr2:38767123-38768717	XLOC_002054

No data

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

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1543880	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022945	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17576044	0.87[YRI][hapmap]
rs17603782	1.00[MEX][hapmap]
rs2304005	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3213852	1.00[ASN][1000 genomes]
rs41446253	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55785223	0.87[AMR][1000 genomes]
rs55833813	0.87[AMR][1000 genomes]
rs55957936	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56251362	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56956410	0.87[AMR][1000 genomes]
rs58441205	1.00[ASN][1000 genomes]
rs59114683	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60475078	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544167	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6727765	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6732384	0.85[AMR][1000 genomes]
rs72895897	0.87[AMR][1000 genomes]
rs72897608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72897610	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905837	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72905839	0.87[AMR][1000 genomes]
rs72905843	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905844	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905847	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72905860	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72905861	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72905863	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72905868	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72905869	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72905871	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72905880	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905899	1.00[ASN][1000 genomes]
rs73929040	0.87[AMR][1000 genomes]
rs73929050	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73929059	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73929077	1.00[AMR][1000 genomes]
rs73931606	0.85[AMR][1000 genomes]
rs7578356	1.00[MEX][hapmap]
rs7579589	0.85[AMR][1000 genomes]
rs7584862	1.00[MEX][hapmap]
rs7586241	0.81[YRI][hapmap]
rs7594264	0.85[AMR][1000 genomes]
rs9789532	1.00[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6732743	RNF212	trans	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

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

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