Variant report

Variant	rs10838524
Chromosome Location	chr11:45870177-45870178
allele	A/G
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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:45823557..45830738-chr11:45863397..45877001,19	MCF-7	breast:
2	chr11:45869438..45872196-chr11:45903876..45906831,3	K562	blood:
3	chr11:45869749..45872196-chr11:45903148..45905376,2	K562	blood:
4	chr11:45868765..45870683-chr11:45944601..45946304,2	MCF-7	breast:
5	chr11:45869552..45871506-chr11:46003139..46005373,2	K562	blood:
6	chr11:45868950..45870705-chr11:45892090..45893685,2	K562	blood:
7	chr11:45824002..45829445-chr11:45867072..45871709,12	MCF-7	breast:
8	chr11:45841387..45844353-chr11:45869079..45870612,2	MCF-7	breast:
9	chr11:45867151..45870859-chr11:45942545..45946514,4	K562	blood:
10	chr11:45859074..45860991-chr11:45869177..45870852,2	MCF-7	breast:
11	chr11:45868680..45870553-chr11:45907106..45909020,2	K562	blood:
12	chr11:45869428..45871022-chr11:45916050..45918387,2	MCF-7	breast:
13	chr11:45847212..45849516-chr11:45869124..45870868,2	K562	blood:
14	chr11:45867957..45870667-chr11:45891635..45895689,3	MCF-7	breast:
15	chr11:45867854..45870393-chr11:45906869..45909551,2	MCF-7	breast:
16	chr11:45854327..45856053-chr11:45869325..45871424,2	K562	blood:
17	chr11:45867823..45873583-chr11:45876186..45881298,10	MCF-7	breast:
18	chr11:45868914..45870628-chr11:45938803..45941080,3	MCF-7	breast:
19	chr11:45868118..45870705-chr11:45891795..45893685,3	K562	blood:
20	chr11:45868641..45870553-chr11:45905537..45909020,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000121680	Chromatin interaction
ENSG00000121671	Chromatin interaction
ENSG00000181830	Chromatin interaction
ENSG00000165905	Chromatin interaction
ENSG00000121653	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11038672	1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs11038694	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605924	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607182	0.81[EUR][1000 genomes]
rs11607883	0.95[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12419690	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12794698	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12805422	0.92[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12807179	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1401419	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292910	0.81[CHD][hapmap]
rs34043764	0.81[EUR][1000 genomes]
rs6485644	0.98[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs6485645	0.89[EUR][1000 genomes]
rs6485646	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105751	1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs7112505	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7115753	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7121611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7933420	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7945565	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945689	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10838524	CHST1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45868200-45870200	Active TSS	Fetal Muscle Trunk	muscle
2	chr11:45868400-45870200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:45868400-45870200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:45868400-45870200	Active TSS	Ovary	ovary
5	chr11:45868400-45871200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr11:45868600-45870200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:45868600-45870200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:45868600-45870200	Active TSS	Left Ventricle	heart
9	chr11:45868600-45870200	Active TSS	Right Ventricle	heart
10	chr11:45868600-45870200	Active TSS	NHDF-Ad	bronchial
11	chr11:45868800-45870200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr11:45868800-45870200	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr11:45868800-45870200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:45868800-45870200	Active TSS	Rectal Smooth Muscle	rectum
15	chr11:45868800-45870200	Active TSS	Stomach Mucosa	stomach
16	chr11:45868800-45870400	Active TSS	Pancreas	Pancrea
17	chr11:45869000-45870200	Active TSS	Lung	lung
18	chr11:45869000-45870200	Active TSS	Right Atrium	heart
19	chr11:45869200-45870200	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr11:45869200-45870400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:45869400-45870200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr11:45869400-45870200	Flanking Active TSS	Placenta	Placenta
23	chr11:45869400-45870400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr11:45869400-45870400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:45869400-45870400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr11:45869400-45870600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr11:45869600-45870200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr11:45869600-45870200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr11:45869600-45870200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:45869600-45870200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr11:45869600-45870200	Flanking Active TSS	Thymus	Thymus
32	chr11:45869600-45870200	Flanking Active TSS	HUVEC	blood vessel
33	chr11:45869600-45870400	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr11:45869600-45870400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:45869600-45870400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr11:45869600-45870400	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr11:45869600-45870400	Flanking Active TSS	Fetal Thymus	thymus
38	chr11:45869600-45870400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr11:45869600-45870600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr11:45869600-45870600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr11:45869600-45870600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:45869600-45870600	Flanking Active TSS	Fetal Stomach	stomach
43	chr11:45869600-45870600	Flanking Active TSS	K562	blood
44	chr11:45869600-45870800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr11:45869600-45870800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:45869600-45871000	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr11:45869600-45871000	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr11:45869600-45871000	Flanking Active TSS	Dnd41	blood
49	chr11:45869600-45871200	Flanking Active TSS	Fetal Brain Female	brain
50	chr11:45869800-45870200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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