Variant report

Variant	rs10496038
Chromosome Location	chr2:55340963-55340964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr2:55338384-55341644	IMR90	lung:	n/a	n/a
2	POLR2A	chr2:55338458-55341172	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
2	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
3	chr2:55339781..55342552-chr2:55346442..55349594,4	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11677099	1.00[MEX][hapmap]
rs11677598	1.00[AFR][1000 genomes]
rs11686766	1.00[CEU][hapmap]
rs11686912	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs11696046	1.00[MEX][hapmap]
rs11894868	1.00[MEX][hapmap]
rs12619486	1.00[MEX][hapmap]
rs12995548	1.00[CEU][hapmap]
rs13003020	0.89[CEU][hapmap]
rs13017468	0.89[CEU][hapmap]
rs13021245	1.00[MEX][hapmap]
rs13032294	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs13033042	1.00[MEX][hapmap]
rs2028139	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs34656234	1.00[AFR][1000 genomes]
rs35183885	0.89[CEU][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap]
rs35297827	1.00[AFR][1000 genomes]
rs4318424	1.00[CEU][hapmap]
rs6742306	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs6747466	1.00[CEU][hapmap]
rs71414542	1.00[AFR][1000 genomes]
rs7595814	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][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	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55329600-55342600	Weak transcription	NHEK	skin
2	chr2:55332000-55343400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:55335400-55341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr2:55337200-55341000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:55337400-55342800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:55337400-55342800	Weak transcription	HMEC	breast
8	chr2:55338200-55341200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr2:55338400-55341000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:55338400-55341200	Enhancers	Stomach Mucosa	stomach
11	chr2:55338400-55343400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:55338400-55343400	Enhancers	Primary hematopoietic stem cells	blood
13	chr2:55338600-55341000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:55338600-55341000	Enhancers	Placenta	Placenta
15	chr2:55338600-55341000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr2:55338600-55341000	Enhancers	Right Ventricle	heart
17	chr2:55338600-55341200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr2:55338600-55341200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:55338600-55341400	Flanking Active TSS	HSMMtube	muscle
20	chr2:55338600-55341400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr2:55338600-55341600	Enhancers	Fetal Thymus	thymus
22	chr2:55338600-55343800	Enhancers	Fetal Muscle Leg	muscle
23	chr2:55338800-55341000	Enhancers	Fetal Lung	lung
24	chr2:55339000-55341000	Enhancers	Psoas Muscle	Psoas
25	chr2:55339000-55341200	Enhancers	Primary B cells from cord blood	blood
26	chr2:55339200-55343000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:55339400-55351000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:55339600-55341400	Enhancers	NHDF-Ad	bronchial
29	chr2:55339600-55342200	Weak transcription	Hela-S3	cervix
30	chr2:55339600-55342600	Enhancers	A549	lung
31	chr2:55339600-55345800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:55339600-55345800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:55339600-55345800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:55339600-55346800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:55339600-55347000	Weak transcription	Left Ventricle	heart
36	chr2:55339800-55341000	Enhancers	Osteobl	bone
37	chr2:55339800-55341200	Enhancers	Colon Smooth Muscle	Colon
38	chr2:55339800-55342600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:55339800-55343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:55339800-55343000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:55339800-55344400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:55339800-55345600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:55339800-55345800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:55339800-55347000	Weak transcription	Lung	lung
45	chr2:55340000-55341600	Bivalent Enhancer	HepG2	liver
46	chr2:55340000-55342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:55340000-55343600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:55340000-55343600	Enhancers	NHLF	lung
49	chr2:55340000-55345600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr2:55340200-55341000	Transcr. at gene 5' and 3'	HSMM	muscle

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