Variant report

Variant	rs1401908
Chromosome Location	chr4:57285163-57285164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57284356..57287105-chr4:57332095..57333963,2	K562	blood:
2	chr4:57284634..57287528-chr4:57288727..57291692,2	MCF-7	breast:
3	chr4:57283427..57285263-chr4:57295850..57297831,2	MCF-7	breast:
4	chr4:57283306..57285849-chr4:57301856..57304089,2	MCF-7	breast:
5	chr4:57283528..57287242-chr4:57332184..57336450,3	MCF-7	breast:
6	chr4:57283337..57287999-chr4:57297926..57302779,6	K562	blood:
7	chr4:57265375..57267060-chr4:57284878..57287823,2	K562	blood:
8	chr4:57276645..57279077-chr4:57282984..57285624,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction
ENSG00000268171	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1042040	1.00[CEU][hapmap];0.83[LWK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11538098	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11722404	0.85[EUR][1000 genomes]
rs11728068	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11732985	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11734595	0.85[EUR][1000 genomes]
rs11935357	0.93[EUR][1000 genomes]
rs11937997	0.81[EUR][1000 genomes]
rs11943048	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs13109030	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs13114481	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13122196	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs13122422	0.83[EUR][1000 genomes]
rs13122832	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs13123301	0.85[CEU][hapmap]
rs13123542	0.81[AFR][1000 genomes]
rs13124065	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13129188	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs13131846	0.81[EUR][1000 genomes]
rs13132553	0.82[EUR][1000 genomes]
rs13135151	0.83[EUR][1000 genomes]
rs13140746	0.83[EUR][1000 genomes]
rs13146014	1.00[CEU][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13148435	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs13148656	0.92[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs13150967	0.92[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs1401911	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17086746	0.92[JPT][hapmap]
rs17086755	0.91[JPT][hapmap]
rs17086769	0.92[JPT][hapmap]
rs17086776	0.92[JPT][hapmap]
rs17086786	0.89[JPT][hapmap]
rs17086844	0.92[JPT][hapmap]
rs2030363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292984	1.00[JPT][hapmap]
rs3796543	1.00[JPT][hapmap]
rs3796544	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4074775	0.90[JPT][hapmap]
rs41476944	0.92[JPT][hapmap]
rs6554346	0.83[EUR][1000 genomes]
rs6554347	0.82[CEU][hapmap]
rs6554350	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6554353	0.84[EUR][1000 genomes]
rs6554354	0.92[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs6811153	0.83[EUR][1000 genomes]
rs6811616	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6811652	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6812222	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6815480	0.83[EUR][1000 genomes]
rs6818283	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6818340	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6820922	0.94[EUR][1000 genomes]
rs6854326	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6857561	0.82[EUR][1000 genomes]
rs7437329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7654543	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7656361	0.81[EUR][1000 genomes]
rs7673373	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7682041	0.81[EUR][1000 genomes]
rs7682608	0.82[EUR][1000 genomes]
rs7695701	0.81[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7699157	0.84[EUR][1000 genomes]
rs956275	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs9995463	0.92[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1401908	AASDH	cis	parietal	SCAN
rs1401908	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs1401908	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs1401908	AASDH	cis	cerebellum	SCAN
rs1401908	AASDH	cis	multi-tissue	Pritchard
rs1401908	RPL21P44	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
3	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
7	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
8	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:57274000-57287000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:57274000-57290600	Weak transcription	GM12878-XiMat	blood
11	chr4:57274200-57287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:57274200-57296400	Weak transcription	Dnd41	blood
13	chr4:57277000-57287200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:57277000-57287200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:57277000-57287400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:57277000-57289800	Weak transcription	Fetal Stomach	stomach
17	chr4:57277000-57290000	Weak transcription	Aorta	Aorta
18	chr4:57277000-57290200	Weak transcription	Ovary	ovary
19	chr4:57277000-57290800	Weak transcription	Right Atrium	heart
20	chr4:57277000-57294200	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:57277000-57299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:57277000-57300000	Weak transcription	HSMM	muscle
23	chr4:57277800-57298000	Weak transcription	A549	lung
24	chr4:57278000-57286800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:57278000-57286800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:57278000-57290400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:57278000-57291600	Weak transcription	Brain Anterior Caudate	brain
28	chr4:57278000-57291600	Weak transcription	HepG2	liver
29	chr4:57278000-57294000	Weak transcription	HUVEC	blood vessel
30	chr4:57278000-57299200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:57278200-57300200	Weak transcription	Fetal Kidney	kidney
32	chr4:57278200-57300200	Weak transcription	NHDF-Ad	bronchial
33	chr4:57278400-57290800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:57278600-57286800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:57278600-57287000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:57278600-57290600	Weak transcription	K562	blood
37	chr4:57279400-57287200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:57280600-57291800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr4:57280600-57292600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:57280600-57297800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:57280800-57287000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:57280800-57299400	Weak transcription	Fetal Lung	lung
43	chr4:57281000-57295000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:57281000-57299200	Weak transcription	HMEC	breast
45	chr4:57281600-57291600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:57281800-57290800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr4:57282800-57287000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:57283200-57286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr4:57284000-57294600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:57284800-57300400	Weak transcription	Fetal Intestine Small	intestine

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