Variant report

Variant	rs3748610
Chromosome Location	chr1:151542099-151542100
allele	A/C
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151482728..151486205-chr1:151540004..151544693,5	MCF-7	breast:
2	chr1:151526616..151529320-chr1:151540801..151542682,2	MCF-7	breast:
3	chr1:151428600..151431654-chr1:151540611..151542217,3	MCF-7	breast:
4	chr1:151511950..151514146-chr1:151540485..151542423,2	MCF-7	breast:
5	chr1:151514211..151516187-chr1:151541825..151543936,2	MCF-7	breast:
6	chr1:151540484..151542860-chr1:151546818..151548619,2	MCF-7	breast:
7	chr1:151415037..151418672-chr1:151540855..151543962,3	MCF-7	breast:
8	chr1:151531743..151533271-chr1:151541571..151544265,2	MCF-7	breast:
9	chr1:151534117..151538483-chr1:151538584..151542578,5	MCF-7	breast:
10	chr1:151535253..151539972-chr1:151541025..151545495,6	MCF-7	breast:
11	chr1:151541632..151544049-chr1:151545591..151549035,3	MCF-7	breast:
12	chr1:151520214..151522047-chr1:151540698..151542766,2	MCF-7	breast:
13	chr1:151539929..151545457-chr1:151553538..151558687,9	MCF-7	breast:
14	chr1:151522558..151525413-chr1:151540386..151543231,3	MCF-7	breast:
15	chr1:151537367..151539480-chr1:151541613..151543585,2	K562	blood:
16	chr1:151510961..151514204-chr1:151540033..151544637,10	MCF-7	breast:
17	chr1:151514171..151515908-chr1:151540816..151544051,3	MCF-7	breast:
18	chr1:151539778..151542331-chr1:151689893..151691713,2	MCF-7	breast:
19	chr1:151539684..151544323-chr1:151552691..151557234,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143367	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143375	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10218788	0.92[EUR][1000 genomes]
rs10494267	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11807809	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12090862	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12564097	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12723898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12734011	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12734511	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12747024	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12747990	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12751350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1539490	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891592	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1935886	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34180474	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34690266	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3748608	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970919	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6587605	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6675022	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679183	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6691958	0.95[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs6698282	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704177	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7554707	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3748610	TUFT1	cis	parietal	SCAN
rs3748610	MRPS21	cis	parietal	SCAN
rs3748610	FLG2	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151514400-151556800	Weak transcription	Fetal Brain Male	brain
2	chr1:151520600-151545200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:151521800-151559000	Weak transcription	Small Intestine	intestine
4	chr1:151531800-151542200	Strong transcription	HSMM	muscle
5	chr1:151532000-151542200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:151532200-151546400	Weak transcription	Spleen	Spleen
7	chr1:151532600-151551200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:151533000-151557200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:151533800-151561600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:151534200-151542200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:151534200-151542400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:151534200-151549400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:151534200-151550200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr1:151535000-151547000	Strong transcription	HSMMtube	muscle
15	chr1:151535600-151547000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:151535800-151561800	Weak transcription	Brain Substantia Nigra	brain
17	chr1:151536000-151544600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:151536000-151546800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:151536000-151547000	Strong transcription	Placenta	Placenta
20	chr1:151536400-151546000	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr1:151537000-151556800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:151537400-151556000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:151537400-151558400	Weak transcription	Fetal Kidney	kidney
24	chr1:151537600-151542200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:151537600-151546800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:151538000-151546400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:151538000-151557400	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:151538200-151543800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:151538200-151545200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:151538600-151546800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:151538800-151544800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:151538800-151548800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:151539000-151546400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:151539000-151556400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:151539000-151557000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:151539600-151545200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:151539600-151546600	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:151539600-151547000	Weak transcription	Brain Anterior Caudate	brain
39	chr1:151539600-151555400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:151540000-151542200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:151540000-151542200	Weak transcription	Left Ventricle	heart
42	chr1:151540000-151546400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:151540200-151542600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:151540200-151542800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:151540200-151545400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:151540400-151544200	Enhancers	HMEC	breast
47	chr1:151540600-151542200	Genic enhancers	A549	lung
48	chr1:151540600-151544400	Genic enhancers	NHEK	skin
49	chr1:151540800-151542400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:151540800-151542400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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