Variant report

Variant	rs6731862
Chromosome Location	chr2:47201099-47201100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47185770..47187647-chr2:47200287..47201915,2	K562	blood:
2	chr2:47192520..47194152-chr2:47197519..47201107,3	K562	blood:
3	chr2:47198749..47201543-chr2:47204357..47206342,2	MCF-7	breast:
4	chr2:47184744..47187647-chr2:47199818..47201787,2	K562	blood:
5	chr2:47200108..47202045-chr2:47202307..47204187,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10183233	0.88[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11125106	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]
rs11125107	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs11125108	0.90[ASN][1000 genomes]
rs1122516	0.84[CHB][hapmap]
rs11680029	0.88[ASN][1000 genomes]
rs11681157	0.87[ASN][1000 genomes]
rs11685461	0.84[CHB][hapmap]
rs11685605	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs11883507	0.84[ASN][1000 genomes]
rs12052808	0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12712982	0.84[CHB][hapmap]
rs12712983	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs13002842	0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs13014374	0.89[CHB][hapmap]
rs13395498	0.89[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs13406452	0.92[ASN][1000 genomes]
rs1433772	0.85[ASN][1000 genomes]
rs1433773	0.89[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs17480779	0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1865262	0.84[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2347260	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2881587	0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs35779609	0.90[ASN][1000 genomes]
rs4952858	0.83[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6544943	0.84[CHB][hapmap]
rs6544944	0.84[CHB][hapmap]
rs6713810	0.84[CHB][hapmap]
rs6716882	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731875	0.95[ASN][1000 genomes]
rs6734201	0.82[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs736683	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs746915	0.92[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7558171	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs7558196	0.84[CHB][hapmap]
rs7560371	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7602813	0.84[CHB][hapmap]
rs877047	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs877048	0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs892380	0.84[CHB][hapmap]
rs892381	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs993847	0.84[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
rs6731862	HDGFRP3	trans	lymphoblastoid	seeQTL
rs6731862	MCFD2	cis	parietal	SCAN

Chromatin state (count:116 , 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	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:47184600-47205000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:47185000-47206000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:47185200-47210200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:47185400-47205800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:47185400-47210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:47186400-47205600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:47186800-47205200	Weak transcription	Gastric	stomach
12	chr2:47186800-47205800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:47187400-47206000	Weak transcription	Fetal Brain Female	brain
14	chr2:47187800-47203200	Weak transcription	Brain Germinal Matrix	brain
15	chr2:47187800-47210200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:47188000-47205200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:47188000-47207000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:47193800-47204000	Strong transcription	Primary T cells from cord blood	blood
19	chr2:47195200-47202200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr2:47195400-47202000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:47195600-47205200	Weak transcription	Fetal Lung	lung
22	chr2:47195600-47210400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:47195600-47212800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:47195800-47202000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:47195800-47202000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:47196000-47205800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:47196400-47211800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:47196600-47227800	Strong transcription	Dnd41	blood
29	chr2:47197200-47202000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:47197200-47203200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:47197600-47206000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:47197800-47201200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:47197800-47201600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:47197800-47202000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:47197800-47202000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:47197800-47202200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:47198000-47201800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:47198000-47203600	Weak transcription	Aorta	Aorta
39	chr2:47198000-47204000	Weak transcription	Left Ventricle	heart
40	chr2:47198000-47209800	Weak transcription	Right Atrium	heart
41	chr2:47198200-47201200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:47198200-47201200	Weak transcription	Ovary	ovary
43	chr2:47198200-47201800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:47198200-47202200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:47198200-47202200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr2:47198200-47202200	Weak transcription	NH-A	brain
47	chr2:47198200-47203400	Weak transcription	Lung	lung
48	chr2:47198200-47203800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:47198200-47205800	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:47198200-47206800	Weak transcription	Right Ventricle	heart

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