Variant report

Variant	rs9808377
Chromosome Location	chr2:179421694-179421695
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:179419227..179421717-chr2:179434065..179436683,2	K562	blood:
2	chr2:179421259..179423341-chr2:179461090..179463054,2	K562	blood:
3	chr2:179408014..179409933-chr2:179421208..179423419,2	K562	blood:
4	chr2:179315026..179317909-chr2:179421262..179423691,2	K562	blood:
5	chr2:179418405..179420692-chr2:179421306..179423003,2	K562	blood:
6	chr2:179417332..179419905-chr2:179420592..179422806,2	K562	blood:
7	chr2:179421259..179423141-chr2:179424971..179426948,2	K562	blood:
8	chr2:179413182..179414824-chr2:179420197..179422852,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204311	Chromatin interaction
ENSG00000180228	Chromatin interaction
ENSG00000270277	Chromatin interaction
ENSG00000237298	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1001238	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12052983	0.81[CHB][hapmap]
rs12693162	0.94[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1560221	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16866342	0.85[CHB][hapmap]
rs16866400	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16866420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1978580	0.81[CHB][hapmap]
rs2042995	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2042996	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2163009	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2249737	0.81[CHB][hapmap]
rs2288571	0.81[JPT][hapmap]
rs2303537	0.81[CHB][hapmap]
rs2303838	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs2366751	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2472751	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562845	0.88[TSI][hapmap]
rs2742351	0.95[CHB][hapmap]
rs35504893	0.96[ASN][1000 genomes]
rs36113194	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3731746	0.81[JPT][hapmap]
rs3731750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731754	0.85[CHB][hapmap]
rs3769864	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769866	0.86[CHB][hapmap]
rs3813250	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3820978	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829746	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4894029	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4894030	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs6704545	0.86[CHB][hapmap]
rs6712785	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6723399	0.89[ASN][1000 genomes]
rs6735077	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6753709	0.82[CHB][hapmap]
rs7600176	0.82[CHB][hapmap]
rs8179648	0.85[JPT][hapmap]
rs890578	0.81[JPT][hapmap]
rs957875	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs967507	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv2757841	chr2:179409072-179608242	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759103	chr2:179409072-179608242	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9808377	HOXD9	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179429400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:179388800-179441800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:179388800-179448800	Weak transcription	Small Intestine	intestine
4	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:179389400-179428200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:179390600-179426400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:179393800-179439800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:179395400-179423000	Strong transcription	Fetal Muscle Trunk	muscle
9	chr2:179396000-179422400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:179396000-179445400	Strong transcription	Right Ventricle	heart
11	chr2:179396600-179432400	Weak transcription	Fetal Kidney	kidney
12	chr2:179405200-179427000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:179406600-179422800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr2:179408000-179503000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:179408200-179436200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:179409200-179439200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:179410800-179422200	Weak transcription	Placenta	Placenta
18	chr2:179410800-179428600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:179411000-179440000	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:179411000-179466000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:179411200-179440200	Weak transcription	Colonic Mucosa	Colon
22	chr2:179411600-179429400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:179412000-179441000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:179413200-179424800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:179413200-179435000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:179413400-179437400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:179413600-179422200	Strong transcription	Primary T cells from cord blood	blood
28	chr2:179413600-179424200	Strong transcription	Fetal Muscle Leg	muscle
29	chr2:179413600-179427800	Weak transcription	Esophagus	oesophagus
30	chr2:179413600-179438200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:179413600-179438800	Weak transcription	Brain Anterior Caudate	brain
32	chr2:179413600-179440000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:179413800-179425400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:179413800-179426400	Weak transcription	Fetal Lung	lung
35	chr2:179413800-179427800	Weak transcription	Gastric	stomach
36	chr2:179413800-179436800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:179414000-179424800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:179414000-179428200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:179414000-179439000	Weak transcription	Brain Angular Gyrus	brain
40	chr2:179414000-179443400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:179414200-179422200	Weak transcription	Fetal Stomach	stomach
42	chr2:179414200-179424800	Weak transcription	Fetal Brain Male	brain
43	chr2:179414200-179426400	Weak transcription	Thymus	Thymus
44	chr2:179414200-179427800	Weak transcription	Dnd41	blood
45	chr2:179414200-179428000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:179414200-179428000	Weak transcription	Liver	Liver
47	chr2:179414200-179431200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:179414200-179434800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:179414200-179435200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:179414200-179439200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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