Variant report

Variant	rs3754741
Chromosome Location	chr2:174053219-174053220
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	chr2:174047844..174049361-chr2:174051278..174054008,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10930579	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615166	0.83[ASN][1000 genomes]
rs12986917	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs12987496	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs12989116	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12990553	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12997078	0.85[ASN][1000 genomes]
rs12998711	0.83[ASN][1000 genomes]
rs13004212	0.80[ASN][1000 genomes]
rs13008554	0.86[ASN][1000 genomes]
rs13017210	0.82[ASN][1000 genomes]
rs13017438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022800	0.90[CHB][hapmap]
rs13029949	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs13032010	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16861278	0.89[CHB][hapmap]
rs17302977	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs17761169	0.88[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2076857	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278883	0.82[CHB][hapmap]
rs2289397	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289399	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34472765	0.80[ASN][1000 genomes]
rs34658268	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34702663	0.81[ASN][1000 genomes]
rs35250703	0.80[ASN][1000 genomes]
rs36102078	0.80[ASN][1000 genomes]
rs36103648	0.85[ASN][1000 genomes]
rs3754743	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3754744	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.94[ASN][1000 genomes]
rs3769157	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769161	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3769167	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3769192	0.82[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs3769194	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs3769203	0.90[CHB][hapmap]
rs4972533	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55913048	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56151459	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56193548	0.80[ASN][1000 genomes]
rs6433395	0.90[CHB][hapmap]
rs71417423	0.83[ASN][1000 genomes]
rs72905080	0.80[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3754741	GORASP2	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174026000-174069000	Weak transcription	Primary B cells from cord blood	blood
2	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
3	chr2:174028400-174054600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:174037400-174054600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:174046200-174054200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:174046200-174054400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:174046200-174055800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:174046400-174075800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:174046600-174055800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:174047000-174062800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:174047600-174056400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:174047600-174060800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:174047600-174062800	Weak transcription	GM12878-XiMat	blood
14	chr2:174047800-174065800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:174048600-174095200	Weak transcription	Thymus	Thymus
16	chr2:174049000-174070600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:174049200-174053600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:174049200-174070200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:174049200-174083200	Weak transcription	Small Intestine	intestine
20	chr2:174049400-174054200	Weak transcription	Fetal Intestine Large	intestine
21	chr2:174049400-174054800	Weak transcription	Dnd41	blood
22	chr2:174049400-174055800	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:174049400-174056000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:174049400-174058400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:174049400-174060600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:174049400-174060800	Weak transcription	Lung	lung
27	chr2:174049400-174060800	Weak transcription	Right Ventricle	heart
28	chr2:174049400-174078200	Weak transcription	HUVEC	blood vessel
29	chr2:174049600-174056000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:174049600-174056200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:174049600-174062800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:174049600-174074400	Weak transcription	Fetal Stomach	stomach
33	chr2:174049600-174079800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:174049800-174062600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:174050000-174054600	Weak transcription	Psoas Muscle	Psoas
36	chr2:174050200-174062800	Weak transcription	HepG2	liver
37	chr2:174051000-174054600	Weak transcription	Fetal Thymus	thymus
38	chr2:174051600-174053600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr2:174051600-174065200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr2:174051800-174053600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:174051800-174053600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:174051800-174053600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr2:174051800-174053600	Genic enhancers	NHLF	lung
44	chr2:174051800-174053600	Enhancers	Osteobl	bone
45	chr2:174052000-174053400	Enhancers	Stomach Smooth Muscle	stomach
46	chr2:174052000-174053400	Enhancers	NH-A	brain
47	chr2:174052000-174056200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr2:174052000-174059600	Weak transcription	Aorta	Aorta
49	chr2:174052000-174063000	Weak transcription	Placenta	Placenta
50	chr2:174052200-174053400	Enhancers	Fetal Lung	lung

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