Variant report

Variant	rs6005863
Chromosome Location	chr22:29156448-29156449
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29156021..29156832-chr6:26157915..26158484,2	MCF-7	breast:
2	chr22:29090716..29093047-chr22:29154418..29156765,2	K562	blood:
3	chr22:29155529..29158980-chr22:29193770..29197123,3	MCF-7	breast:
4	chr22:29156118..29157971-chr22:29167441..29169542,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158373	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000159873	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1033667	0.81[JPT][hapmap]
rs5752783	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs5752786	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5752791	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762768	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5762776	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762777	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5762783	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5997397	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005862	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005864	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs738722	0.81[JPT][hapmap]
rs9608698	0.87[CEU][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs9613668	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv516312	chr22:29153759-29160314	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6005863	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29143400-29156600	Weak transcription	Brain Substantia Nigra	brain
2	chr22:29143600-29160000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:29145400-29157200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr22:29145800-29156600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr22:29145800-29168000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr22:29146000-29156600	Weak transcription	Adipose Nuclei	Adipose
7	chr22:29146800-29156600	Weak transcription	Primary T cells from cord blood	blood
8	chr22:29146800-29156600	Weak transcription	Fetal Intestine Large	intestine
9	chr22:29148000-29164400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr22:29148000-29167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr22:29149200-29156800	Weak transcription	Fetal Lung	lung
12	chr22:29149400-29156800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr22:29149600-29165400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr22:29149800-29156600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr22:29150200-29157400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr22:29150600-29157000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr22:29154200-29156600	Weak transcription	Fetal Muscle Leg	muscle
18	chr22:29154400-29156600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr22:29154400-29167400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr22:29155400-29156800	Enhancers	HepG2	liver
21	chr22:29155600-29156600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr22:29155600-29156600	Enhancers	HSMMtube	muscle
23	chr22:29155600-29156800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr22:29155600-29157000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr22:29155600-29157600	Enhancers	Primary B cells from peripheral blood	blood
26	chr22:29155800-29156600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr22:29155800-29156600	Enhancers	Brain Germinal Matrix	brain
28	chr22:29155800-29156600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr22:29155800-29156800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr22:29155800-29156800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr22:29155800-29157000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr22:29155800-29157000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr22:29156000-29156600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr22:29156000-29156800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr22:29156000-29156800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr22:29156000-29156800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr22:29156000-29156800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr22:29156000-29156800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr22:29156000-29156800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr22:29156000-29156800	Flanking Active TSS	GM12878-XiMat	blood
41	chr22:29156000-29157000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr22:29156200-29156600	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr22:29156200-29156600	Flanking Active TSS	Fetal Brain Female	brain
44	chr22:29156200-29156800	Enhancers	Primary hematopoietic stem cells	blood
45	chr22:29156200-29156800	Enhancers	Brain Cingulate Gyrus	brain
46	chr22:29156200-29157000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr22:29156200-29157200	Enhancers	Primary B cells from cord blood	blood
48	chr22:29156400-29156600	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr22:29156400-29156600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr22:29156400-29156600	Active TSS	H9 Cell Line	embryonic stem cell

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