Variant report

Variant	rs3829746
Chromosome Location	chr2:179427536-179427537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179414417..179416892-chr2:179427322..179430002,3	K562	blood:
2	chr2:179422059..179424305-chr2:179427109..179429987,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1001238	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12052983	0.81[CHB][hapmap]
rs12693162	1.00[ASW][hapmap];0.83[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1560221	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16866342	0.85[CHB][hapmap]
rs16866400	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16866420	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1978580	0.81[CHB][hapmap]
rs2042995	0.88[ASW][hapmap];0.94[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2042996	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2163009	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288571	0.81[JPT][hapmap]
rs2303537	0.81[CHB][hapmap]
rs2303838	0.81[JPT][hapmap]
rs2366751	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2472751	0.94[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562845	0.85[TSI][hapmap]
rs2742351	0.90[CHB][hapmap]
rs35504893	0.95[ASN][1000 genomes]
rs36113194	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3731746	0.81[JPT][hapmap]
rs3731750	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3731754	0.85[CHB][hapmap]
rs3769864	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769866	0.86[CHB][hapmap]
rs3813250	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820978	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4894029	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4894030	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs6704545	0.86[CHB][hapmap]
rs6712785	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6723399	0.88[ASN][1000 genomes]
rs6735077	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6753709	0.82[CHB][hapmap]
rs7600176	0.82[CHB][hapmap]
rs8179648	0.85[JPT][hapmap]
rs890578	0.81[JPT][hapmap]
rs957875	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs967507	0.86[CHB][hapmap]
rs9808377	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]

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
rs3829746	HOXD9	cis	parietal	SCAN

Chromatin state (count:82 , 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	chr2:179393800-179439800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:179396000-179445400	Strong transcription	Right Ventricle	heart
8	chr2:179396600-179432400	Weak transcription	Fetal Kidney	kidney
9	chr2:179408000-179503000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:179408200-179436200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:179409200-179439200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:179410800-179428600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:179411000-179440000	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:179411000-179466000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:179411200-179440200	Weak transcription	Colonic Mucosa	Colon
16	chr2:179411600-179429400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:179412000-179441000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:179413200-179435000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:179413400-179437400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:179413600-179427800	Weak transcription	Esophagus	oesophagus
21	chr2:179413600-179438200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:179413600-179438800	Weak transcription	Brain Anterior Caudate	brain
23	chr2:179413600-179440000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:179413800-179427800	Weak transcription	Gastric	stomach
25	chr2:179413800-179436800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:179414000-179428200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:179414000-179439000	Weak transcription	Brain Angular Gyrus	brain
28	chr2:179414000-179443400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:179414200-179427800	Weak transcription	Dnd41	blood
30	chr2:179414200-179428000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:179414200-179428000	Weak transcription	Liver	Liver
32	chr2:179414200-179431200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:179414200-179434800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:179414200-179435200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:179414200-179439200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:179414800-179471800	Weak transcription	Brain Substantia Nigra	brain
37	chr2:179416000-179430200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:179417600-179427600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:179417600-179434800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:179417800-179430200	Weak transcription	Adipose Nuclei	Adipose
41	chr2:179417800-179441800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:179418000-179427800	Weak transcription	Spleen	Spleen
43	chr2:179418000-179430200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:179418200-179427800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:179418200-179443200	Weak transcription	NHLF	lung
46	chr2:179418400-179439000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:179418400-179450200	Strong transcription	HSMMtube	muscle
48	chr2:179418600-179427800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:179418600-179434200	Weak transcription	Osteobl	bone
50	chr2:179418800-179428000	Weak transcription	Fetal Thymus	thymus

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