Variant report

Variant	rs4894029
Chromosome Location	chr2:179447848-179447849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179442770..179444803-chr2:179445864..179448821,2	K562	blood:
2	chr2:179440588..179442582-chr2:179446121..179449484,3	K562	blood:

Variant related genes	Relation type
ENSG00000271011	Chromatin interaction
ENSG00000270574	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];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12052983	0.81[CHB][hapmap]
rs12693162	0.94[ASW][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1560221	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16866342	0.85[CHB][hapmap]
rs16866400	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16866420	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1978580	0.81[CHB][hapmap]
rs2042995	0.94[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2042996	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2163009	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288571	0.81[JPT][hapmap]
rs2303537	0.81[CHB][hapmap]
rs2303828	0.80[TSI][hapmap]
rs2303838	0.81[JPT][hapmap];0.83[TSI][hapmap]
rs2366751	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[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]
rs2472751	1.00[ASW][hapmap];0.84[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562845	0.91[TSI][hapmap]
rs2742351	0.90[CHB][hapmap]
rs35504893	0.89[ASN][1000 genomes]
rs36113194	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3731746	0.81[JPT][hapmap]
rs3731750	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731754	0.85[CHB][hapmap]
rs3769864	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769866	0.86[CHB][hapmap]
rs3813250	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3820978	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3829746	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	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6723399	0.83[ASN][1000 genomes]
rs6735077	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6753709	0.82[CHB][hapmap]
rs7600176	0.82[CHB][hapmap]
rs8179648	0.85[JPT][hapmap]
rs890578	0.81[JPT][hapmap]
rs957875	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs967507	0.86[CHB][hapmap]
rs9808377	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]

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	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
2	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
3	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
4	nsv1000642	chr2:179438866-179503211	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4894029	HOXD9	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179448800	Weak transcription	Small Intestine	intestine
2	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:179408000-179503000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:179411000-179466000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:179414800-179471800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:179418400-179450200	Strong transcription	HSMMtube	muscle
7	chr2:179428400-179478600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:179429400-179448400	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:179430800-179480000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:179434800-179450000	Strong transcription	Fetal Intestine Large	intestine
11	chr2:179435200-179469800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:179435400-179450200	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr2:179436600-179463400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:179437600-179461400	Strong transcription	Primary B cells from cord blood	blood
15	chr2:179437600-179478800	Weak transcription	Esophagus	oesophagus
16	chr2:179437800-179465600	Strong transcription	Left Ventricle	heart
17	chr2:179438000-179467600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:179438200-179455600	Weak transcription	GM12878-XiMat	blood
19	chr2:179438200-179467200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr2:179438200-179474800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:179438400-179518200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:179439200-179452800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:179439200-179452800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:179439400-179451800	Strong transcription	Fetal Heart	heart
25	chr2:179439600-179455400	Weak transcription	Fetal Brain Male	brain
26	chr2:179440200-179474400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:179440400-179467600	Strong transcription	Fetal Muscle Leg	muscle
28	chr2:179440600-179449600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:179440600-179478800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:179440600-179494000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:179440600-179505200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:179440800-179468200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:179441000-179449200	Weak transcription	Brain Angular Gyrus	brain
34	chr2:179441200-179455000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:179441400-179468600	Weak transcription	Gastric	stomach
36	chr2:179441400-179498800	Weak transcription	Brain Anterior Caudate	brain
37	chr2:179441600-179449800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:179441600-179495000	Weak transcription	Fetal Intestine Small	intestine
39	chr2:179441800-179448000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:179441800-179469400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:179441800-179471600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:179442000-179449000	Weak transcription	Dnd41	blood
43	chr2:179442000-179484200	Weak transcription	Colonic Mucosa	Colon
44	chr2:179442200-179448400	Weak transcription	Liver	Liver
45	chr2:179442200-179451800	Weak transcription	Fetal Lung	lung
46	chr2:179442200-179455400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:179442200-179455800	Weak transcription	Spleen	Spleen
48	chr2:179442200-179463200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:179442200-179464000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:179442200-179466400	Weak transcription	K562	blood

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