Variant report

Variant	rs3754747
Chromosome Location	chr2:173965296-173965297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173965020..173969595-chr2:173970768..173975249,5	K562	blood:
2	chr2:173959127..173960788-chr2:173963546..173966177,2	K562	blood:
3	chr2:173958321..173962110-chr2:173963955..173966177,3	K562	blood:
4	chr2:173939358..173940989-chr2:173963440..173965310,2	K562	blood:
5	chr2:173955322..173959016-chr2:173963058..173965750,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10497402	0.94[CHD][hapmap]
rs11680555	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11687539	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12463612	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs13004345	0.83[LWK][hapmap]
rs1551249	0.83[CEU][hapmap]
rs16861363	0.88[CHD][hapmap]
rs17710065	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17710437	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1809139	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1837470	0.83[LWK][hapmap]
rs1973037	0.83[CEU][hapmap]
rs2043950	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs3754749	0.81[CEU][hapmap]
rs3769159	0.88[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs3769162	0.88[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap]
rs3769163	1.00[JPT][hapmap]
rs3769184	0.83[LWK][hapmap]
rs3769201	0.82[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs3769213	0.83[CEU][hapmap]
rs3820835	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4344898	0.84[LWK][hapmap]
rs4972529	0.88[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs62175799	0.81[EUR][1000 genomes]
rs6433392	0.85[CEU][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs6717529	0.83[CEU][hapmap]
rs6717735	0.83[CEU][hapmap]
rs6742219	0.86[CEU][hapmap]
rs6759847	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs722864	0.91[CHB][hapmap];0.81[TSI][hapmap]
rs734993	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap]
rs746179	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs7567355	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs7575189	0.84[LWK][hapmap]
rs7599340	0.94[CEU][hapmap]
rs935006	0.93[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs935007	0.87[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3754747	CYBRD1	cis	parietal	SCAN
rs3754747	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173941600-173969600	Weak transcription	Spleen	Spleen
2	chr2:173942800-173971400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:173943000-173971200	Weak transcription	HSMMtube	muscle
4	chr2:173943400-173974200	Weak transcription	Fetal Intestine Large	intestine
5	chr2:173945400-173991200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:173952000-173973400	Weak transcription	Hela-S3	cervix
7	chr2:173952200-173971400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:173953000-173968000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:173953800-173991400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:173955400-173970200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:173955600-173968600	Weak transcription	Placenta	Placenta
12	chr2:173955600-173971800	Weak transcription	Lung	lung
13	chr2:173955600-173972000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:173955600-173984000	Weak transcription	Gastric	stomach
15	chr2:173955800-173977200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:173956200-173969000	Weak transcription	NH-A	brain
17	chr2:173956600-173971600	Weak transcription	Fetal Thymus	thymus
18	chr2:173957000-173966800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:173957000-173974400	Weak transcription	Fetal Stomach	stomach
20	chr2:173957600-173972000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:173957800-173973400	Weak transcription	Fetal Lung	lung
22	chr2:173957800-173983800	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:173958000-173983800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:173958200-173965600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:173958200-173966200	Weak transcription	NHDF-Ad	bronchial
26	chr2:173958200-173967000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:173958200-173973800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:173958200-173974000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:173958400-173966200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:173959800-173974200	Weak transcription	HepG2	liver
31	chr2:173961000-173966000	Weak transcription	Liver	Liver
32	chr2:173961400-173973400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:173961800-173970800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:173961800-173974400	Weak transcription	NHLF	lung
35	chr2:173962000-173971000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:173962200-173983800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:173963800-173966000	Weak transcription	A549	lung
38	chr2:173964000-173965400	Enhancers	Colon Smooth Muscle	Colon
39	chr2:173964000-173965800	Enhancers	Stomach Smooth Muscle	stomach
40	chr2:173964200-173965600	Enhancers	Rectal Smooth Muscle	rectum
41	chr2:173964200-173965600	Strong transcription	K562	blood
42	chr2:173964400-173965400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:173964400-173965400	Strong transcription	Dnd41	blood
44	chr2:173964400-173965400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:173964400-173965600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:173964400-173965800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:173964400-173966600	Enhancers	GM12878-XiMat	blood
48	chr2:173964400-173968000	Weak transcription	Primary T cells from cord blood	blood
49	chr2:173964600-173965400	Strong transcription	HUVEC	blood vessel
50	chr2:173964600-173965600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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