Variant report

Variant	rs13424641
Chromosome Location	chr2:38824839-38824840
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

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

No data

(count:17 , 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	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
8	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
9	chr2:38824026..38825901-chr2:38962946..38965190,2	K562	blood:
10	chr2:38824210..38826669-chr2:38912161..38913673,2	MCF-7	breast:
11	chr2:38820462..38822126-chr2:38823935..38825729,2	MCF-7	breast:
12	chr2:38823862..38826061-chr2:38919360..38922289,2	K562	blood:
13	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
14	chr2:38823625..38826319-chr2:38903588..38906507,3	K562	blood:
15	chr2:38824770..38827325-chr2:38977013..38980268,3	MCF-7	breast:
16	chr2:38821957..38830238-chr2:38965333..38974515,17	K562	blood:
17	chr2:38823851..38826080-chr2:38908814..38911340,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235586	TF binding region
ENSG00000235586	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000143891	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10166466	0.84[AFR][1000 genomes]
rs10186867	1.00[AFR][1000 genomes]
rs10192837	0.95[AFR][1000 genomes]
rs10197071	0.95[AFR][1000 genomes]
rs10198949	0.89[AFR][1000 genomes]
rs10204707	0.89[AFR][1000 genomes]
rs10204840	1.00[AFR][1000 genomes]
rs13388732	1.00[AFR][1000 genomes]
rs13391054	0.84[AFR][1000 genomes]
rs13391755	1.00[AFR][1000 genomes]
rs13392719	1.00[AFR][1000 genomes]
rs13401946	0.89[AFR][1000 genomes]
rs13404643	0.89[AFR][1000 genomes]
rs13413591	1.00[AFR][1000 genomes]
rs13423067	1.00[AFR][1000 genomes]
rs13427158	0.89[AFR][1000 genomes]
rs17022981	0.89[AFR][1000 genomes]
rs17022992	0.89[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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