Variant report

Variant	rs7528275
Chromosome Location	chr1:151103537-151103538
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:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151102270..151104122-chr1:151117546..151119575,3	K562	blood:
2	chr1:151100859..151103920-chr1:151107452..151111935,4	MCF-7	breast:
3	chr1:151099788..151103928-chr1:151106315..151110197,5	K562	blood:
4	chr1:151101938..151104431-chr1:151107566..151109145,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEMA6C-1	chr1:151102536-151104086	NONHSAT006361
2	lnc-SEMA6C-1	chr1:151102551-151104086	ENSG00000261168.1

No data

Variant related genes	Relation type
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10888403	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267736	0.82[MEX][hapmap]
rs2864699	1.00[ASN][1000 genomes]
rs4421597	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971009	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6674232	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs67199650	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	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
5	nsv872422	chr1:151098077-151115186	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7528275	UTS2	trans	lymphoblastoid	seeQTL
rs7528275	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs7528275	CDC42SE1	cis	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
2	chr1:151061800-151105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:151079800-151106200	Weak transcription	HSMMtube	muscle
4	chr1:151079800-151114800	Weak transcription	HSMM	muscle
5	chr1:151083400-151103600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:151087000-151103600	Weak transcription	Psoas Muscle	Psoas
7	chr1:151089200-151103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:151090800-151103600	Weak transcription	Esophagus	oesophagus
9	chr1:151090800-151105000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:151091200-151103800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:151091600-151103600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:151091800-151103600	Weak transcription	Gastric	stomach
13	chr1:151091800-151103600	Weak transcription	Lung	lung
14	chr1:151091800-151103600	Weak transcription	Pancreas	Pancrea
15	chr1:151091800-151103600	Weak transcription	Right Ventricle	heart
16	chr1:151092800-151103600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:151095000-151103600	Weak transcription	Liver	Liver
18	chr1:151095600-151103600	Weak transcription	Brain Substantia Nigra	brain
19	chr1:151097800-151103600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:151097800-151105600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:151097800-151106000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:151103000-151104600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:151103200-151103600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
24	chr1:151103200-151103600	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr1:151103200-151103600	Enhancers	Primary hematopoietic stem cells	blood
26	chr1:151103200-151103600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr1:151103200-151103600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:151103200-151103600	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr1:151103200-151103600	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr1:151103200-151103600	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr1:151103200-151103600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr1:151103200-151103800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:151103200-151104400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr1:151103200-151104400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:151103200-151104400	Active TSS	Fetal Kidney	kidney
36	chr1:151103200-151104600	Active TSS	Brain Anterior Caudate	brain
37	chr1:151103200-151106000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
38	chr1:151103400-151103600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr1:151103400-151103600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
40	chr1:151103400-151103600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:151103400-151103600	Active TSS	Primary B cells from cord blood	blood
42	chr1:151103400-151103600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr1:151103400-151103600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:151103400-151103600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:151103400-151103600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:151103400-151103600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:151103400-151103600	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr1:151103400-151103600	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr1:151103400-151103600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr1:151103400-151103600	Active TSS	Fetal Brain Male	brain

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