Variant report

Variant	rs11125106
Chromosome Location	chr2:47192156-47192157
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47164600..47167090-chr2:47190950..47193614,2	K562	blood:
2	chr2:47187193..47190243-chr2:47190337..47193752,4	MCF-7	breast:
3	chr2:47166769..47171325-chr2:47189456..47193821,11	MCF-7	breast:
4	chr2:47191916..47197742-chr2:47401234..47405560,7	MCF-7	breast:
5	chr2:47164675..47170526-chr2:47188235..47196918,12	MCF-7	breast:
6	chr2:47183578..47186392-chr2:47190442..47192561,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000272814	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10183233	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11125107	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11125108	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11680029	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11681157	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12052808	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs12712983	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs13002842	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014374	0.80[CHB][hapmap]
rs13395498	0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs13406452	0.82[ASN][1000 genomes]
rs17480779	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1865262	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2347260	0.81[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2881587	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35779609	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4952858	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6716882	0.89[ASN][1000 genomes]
rs6731862	0.82[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs6731875	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6734201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs736683	0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7560371	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs877047	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs877048	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs993847	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11125106	MCFD2	cis	parietal	SCAN
rs11125106	HDGFRP3	trans	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
2	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:47176400-47192600	Strong transcription	Dnd41	blood
4	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:47177400-47192800	Strong transcription	Fetal Stomach	stomach
6	chr2:47178400-47192800	Strong transcription	Thymus	Thymus
7	chr2:47179000-47192800	Strong transcription	Primary T cells from cord blood	blood
8	chr2:47179200-47195000	Strong transcription	Fetal Thymus	thymus
9	chr2:47179400-47192200	Strong transcription	Primary B cells from cord blood	blood
10	chr2:47179400-47192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:47179400-47193800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr2:47181200-47192200	Strong transcription	GM12878-XiMat	blood
13	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:47183000-47195000	Weak transcription	Small Intestine	intestine
15	chr2:47183400-47192200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr2:47183400-47192600	Strong transcription	Fetal Intestine Large	intestine
17	chr2:47183400-47193400	Strong transcription	Fetal Intestine Small	intestine
18	chr2:47184200-47194400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:47184600-47197600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:47184600-47205000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:47185000-47206000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:47185200-47210200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:47185400-47205800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:47185400-47210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:47185600-47195000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:47185800-47195000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:47186000-47194400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:47186000-47195000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:47186000-47195000	Weak transcription	Left Ventricle	heart
30	chr2:47186200-47200800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:47186400-47205600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:47186600-47194400	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:47186800-47205200	Weak transcription	Gastric	stomach
34	chr2:47186800-47205800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:47187000-47195000	Weak transcription	Right Ventricle	heart
36	chr2:47187200-47197000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:47187400-47206000	Weak transcription	Fetal Brain Female	brain
38	chr2:47187600-47194600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:47187800-47194800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:47187800-47195000	Weak transcription	Colonic Mucosa	Colon
41	chr2:47187800-47203200	Weak transcription	Brain Germinal Matrix	brain
42	chr2:47187800-47210200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:47188000-47194400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:47188000-47194400	Weak transcription	Fetal Lung	lung
45	chr2:47188000-47205200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:47188000-47207000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:47188200-47196800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:47189000-47192200	Genic enhancers	A549	lung
49	chr2:47189000-47192800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:47189000-47192800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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