Variant report

Variant	rs56956410
Chromosome Location	chr2:38766690-38766691
allele	C/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:6)
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	chr2:38766075-38766801	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:38766131-38766697	A549	lung:	n/a	n/a

No data

(count:6 , 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	chr2:38759515..38762169-chr2:38765133..38766792,2	K562	blood:
4	chr2:38762206..38765447-chr2:38765522..38767637,3	K562	blood:
5	chr2:38766439..38768320-chr2:38948180..38949983,2	K562	blood:
6	chr2:38765872..38769105-chr2:38828205..38830691,3	MCF-7	breast:

No data

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

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12614876	1.00[EUR][1000 genomes]
rs12616367	0.83[EUR][1000 genomes]
rs12619629	0.83[EUR][1000 genomes]
rs12621565	0.83[EUR][1000 genomes]
rs12621788	1.00[EUR][1000 genomes]
rs1543880	0.87[AMR][1000 genomes]
rs1543881	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17022945	0.87[AMR][1000 genomes]
rs17576044	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17603782	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34133986	0.83[EUR][1000 genomes]
rs36024292	0.83[EUR][1000 genomes]
rs3765001	0.83[EUR][1000 genomes]
rs41446253	0.87[AMR][1000 genomes]
rs55785223	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55833813	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55957936	0.87[AMR][1000 genomes]
rs56251362	0.87[AMR][1000 genomes]
rs58720388	0.83[EUR][1000 genomes]
rs59065420	0.83[EUR][1000 genomes]
rs59114683	0.87[AMR][1000 genomes]
rs60475078	0.87[AMR][1000 genomes]
rs6727765	0.87[AMR][1000 genomes]
rs6732743	0.87[AMR][1000 genomes]
rs6754893	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72895897	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72897608	0.87[AMR][1000 genomes]
rs72897610	0.87[AMR][1000 genomes]
rs72905831	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72905837	0.87[AMR][1000 genomes]
rs72905839	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72905843	0.87[AMR][1000 genomes]
rs72905844	0.87[AMR][1000 genomes]
rs72905847	0.87[AMR][1000 genomes]
rs72905861	0.87[AMR][1000 genomes]
rs72905863	0.87[AMR][1000 genomes]
rs72905868	0.87[AMR][1000 genomes]
rs72905869	0.87[AMR][1000 genomes]
rs72905871	0.87[AMR][1000 genomes]
rs72905880	0.87[AMR][1000 genomes]
rs73929040	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73929050	0.87[AMR][1000 genomes]
rs73929052	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73929077	0.87[AMR][1000 genomes]
rs7579783	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7584862	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7606515	0.83[EUR][1000 genomes];0.93[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	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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763400-38768000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:38763600-38767200	Weak transcription	Esophagus	oesophagus
3	chr2:38763600-38767400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:38763600-38767600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:38763600-38767800	Weak transcription	Stomach Mucosa	stomach
6	chr2:38763600-38768200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:38763600-38768200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:38763600-38768400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:38763600-38768800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:38763600-38769000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:38763600-38770200	Weak transcription	HSMMtube	muscle
12	chr2:38763600-38771000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:38763800-38767200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:38763800-38767400	Weak transcription	Fetal Brain Female	brain
16	chr2:38763800-38767600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:38763800-38767600	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:38763800-38767600	Weak transcription	Fetal Brain Male	brain
19	chr2:38763800-38767600	Weak transcription	Fetal Intestine Large	intestine
20	chr2:38763800-38767600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:38763800-38767600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:38763800-38767800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:38763800-38767800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:38763800-38767800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:38763800-38768400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:38763800-38768600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:38763800-38769000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:38763800-38769400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:38763800-38769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:38763800-38778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:38764000-38767400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:38764200-38767400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:38764200-38768400	Weak transcription	Liver	Liver
34	chr2:38764200-38769600	Weak transcription	A549	lung
35	chr2:38765600-38768200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr2:38765600-38768400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:38765800-38768000	Enhancers	HepG2	liver
38	chr2:38766400-38766800	Enhancers	H1 Cell Line	embryonic stem cell
39	chr2:38766600-38767600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:38766600-38768200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:38766600-38768200	Weak transcription	Duodenum Mucosa	Duodenum

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