Variant report

Variant	rs3755219
Chromosome Location	chr2:36609376-36609377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36608117..36609788-chr2:36637029..36638848,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11124511	0.84[CEU][hapmap]
rs11901313	0.90[EUR][1000 genomes]
rs12466450	0.84[ASW][hapmap];0.82[CEU][hapmap];0.80[CHD][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs12615281	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs17018679	0.89[EUR][1000 genomes]
rs17018711	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2287084	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3755220	0.92[EUR][1000 genomes]
rs3770918	0.83[EUR][1000 genomes]
rs3770933	0.84[ASW][hapmap];0.83[EUR][1000 genomes]
rs3770934	0.84[ASW][hapmap];0.83[EUR][1000 genomes]
rs3770951	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770957	0.88[CEU][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56295703	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3755219	HEATR5B	cis	parietal	SCAN
rs3755219	GALM	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36586200-36626600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:36599400-36609600	Enhancers	HMEC	breast
3	chr2:36600400-36612000	Genic enhancers	Osteobl	bone
4	chr2:36603800-36612600	Weak transcription	Fetal Brain Female	brain
5	chr2:36604000-36614400	Genic enhancers	HUVEC	blood vessel
6	chr2:36604000-36617000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:36604400-36609400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:36604400-36611200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:36604400-36614000	Weak transcription	HSMMtube	muscle
10	chr2:36604400-36615000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:36604400-36615400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:36604400-36615600	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:36604400-36616400	Weak transcription	Gastric	stomach
14	chr2:36604400-36620600	Weak transcription	Fetal Brain Male	brain
15	chr2:36604400-36640400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:36604400-36640600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:36604600-36614800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:36604600-36617600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:36604600-36620800	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:36604800-36609400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:36604800-36614400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:36605400-36610000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:36606600-36609400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr2:36606600-36609600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:36606600-36609800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:36606600-36610000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr2:36606800-36609400	Enhancers	Fetal Intestine Large	intestine
28	chr2:36607000-36611600	Genic enhancers	NHLF	lung
29	chr2:36607200-36609400	Genic enhancers	Fetal Intestine Small	intestine
30	chr2:36607200-36609600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:36607200-36609800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr2:36607200-36610000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr2:36607200-36610000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:36607200-36610000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:36607200-36610000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:36607400-36609400	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr2:36607600-36609400	Enhancers	Lung	lung
38	chr2:36607600-36610200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr2:36607600-36620800	Weak transcription	Pancreas	Pancrea
40	chr2:36607800-36609600	Enhancers	Adipose Nuclei	Adipose
41	chr2:36607800-36615800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:36608000-36610000	Enhancers	Psoas Muscle	Psoas
43	chr2:36608000-36610800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:36608000-36614000	Weak transcription	Hela-S3	cervix
45	chr2:36608000-36614600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:36608200-36610000	Enhancers	Left Ventricle	heart
47	chr2:36608200-36610000	Enhancers	Right Ventricle	heart
48	chr2:36608200-36612200	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:36608400-36611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:36608600-36609600	Enhancers	HUES64 Cell Line	embryonic stem cell

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