Variant report

Variant	rs11130197
Chromosome Location	chr3:49499167-49499168
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49493317..49496589-chr3:49498122..49502213,4	K562	blood:
2	chr3:49448761..49450977-chr3:49497744..49499450,2	K562	blood:
3	chr3:49494808..49501210-chr3:49505386..49509341,14	MCF-7	breast:
4	chr3:49025870..49028147-chr3:49498822..49500854,2	K562	blood:
5	chr1:14075563..14076244-chr3:49499030..49499576,2	Hela-S3	cervix:
6	chr3:49492720..49494835-chr3:49497709..49500473,4	MCF-7	breast:
7	chr3:49496719..49502585-chr3:49503472..49509213,13	MCF-7	breast:
8	chr3:49498857..49499838-chr3:49507126..49508292,3	MCF-7	breast:
9	chr3:49054424..49056123-chr3:49498434..49500923,2	K562	blood:
10	chr3:49452077..49454427-chr3:49496570..49500540,3	MCF-7	breast:
11	chr3:49499007..49500674-chr3:49711634..49713194,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction
ENSG00000116731	Chromatin interaction
ENSG00000178467	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000223343	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000201301	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11708174	1.00[YRI][hapmap]
rs1522929	1.00[YRI][hapmap]
rs17080495	0.91[YRI][hapmap]
rs17080510	0.91[YRI][hapmap]
rs17080664	0.92[YRI][hapmap]
rs1996874	1.00[YRI][hapmap]
rs2311801	0.91[YRI][hapmap]
rs2329024	1.00[YRI][hapmap]
rs3870334	0.82[YRI][hapmap]
rs3870340	1.00[YRI][hapmap]
rs3912831	1.00[YRI][hapmap]
rs4241409	1.00[YRI][hapmap]
rs4855856	1.00[YRI][hapmap]
rs4855857	1.00[YRI][hapmap]
rs4855879	1.00[YRI][hapmap]
rs6446273	1.00[YRI][hapmap]
rs6446278	0.89[YRI][hapmap]
rs6762593	1.00[YRI][hapmap]
rs6797164	1.00[YRI][hapmap]
rs7646393	1.00[YRI][hapmap]
rs8179172	1.00[YRI][hapmap]

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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11130197	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49490600-49506600	Enhancers	Fetal Muscle Leg	muscle
2	chr3:49491800-49506200	Enhancers	Placenta	Placenta
3	chr3:49492800-49499200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:49494600-49501800	Enhancers	Fetal Muscle Trunk	muscle
5	chr3:49496000-49500000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:49496000-49501400	Enhancers	Pancreas	Pancrea
7	chr3:49496200-49499400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:49496200-49500000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr3:49496200-49500000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49496200-49500000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr3:49496200-49500000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49496200-49500000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:49496200-49500000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:49496200-49500000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:49496200-49500000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:49496200-49500000	Enhancers	HSMM	muscle
17	chr3:49496200-49500000	Enhancers	HSMMtube	muscle
18	chr3:49496200-49500200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:49496200-49501200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:49496200-49501200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:49496200-49501200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:49496400-49499400	Enhancers	Ovary	ovary
23	chr3:49496400-49499600	Enhancers	Lung	lung
24	chr3:49496400-49500000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:49496400-49500000	Enhancers	Fetal Intestine Large	intestine
26	chr3:49496400-49500000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:49496400-49500200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:49496400-49501200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:49496400-49501400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr3:49496800-49499800	Enhancers	Fetal Heart	heart
31	chr3:49496800-49500000	Enhancers	Fetal Intestine Small	intestine
32	chr3:49497400-49506400	Weak transcription	Brain Germinal Matrix	brain
33	chr3:49497600-49500000	Enhancers	Placenta Amnion	Placenta Amnion
34	chr3:49497800-49499800	Enhancers	HMEC	breast
35	chr3:49497800-49500000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:49497800-49500000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:49498000-49499400	Enhancers	GM12878-XiMat	blood
38	chr3:49498000-49500000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:49498000-49500000	Enhancers	Stomach Mucosa	stomach
40	chr3:49498000-49506000	Weak transcription	Fetal Stomach	stomach
41	chr3:49498200-49499600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr3:49498200-49500000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:49498200-49500000	Enhancers	Fetal Thymus	thymus
44	chr3:49498400-49499600	Enhancers	Esophagus	oesophagus
45	chr3:49498400-49499600	Enhancers	Stomach Smooth Muscle	stomach
46	chr3:49498400-49499600	Flanking Active TSS	Hela-S3	cervix
47	chr3:49498400-49500000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:49498400-49500000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr3:49498600-49499400	Flanking Active TSS	HepG2	liver
50	chr3:49498600-49499600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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