Variant report

Variant	rs9450624
Chromosome Location	chr6:87864140-87864141
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr6:87864127-87866285	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr6:87863747-87866254	GM12878	blood:	n/a	chr6:87865268-87865277
3	POLR2A	chr6:87863921-87866992	GM12891	blood:	n/a	n/a
4	MXI1	chr6:87863603-87866820	SK-N-SH	brain:	n/a	chr6:87865268-87865277
5	E2F4	chr6:87863664-87865419	MCF10A-Er-Src	breast:	n/a	chr6:87865155-87865166 chr6:87865152-87865167
6	REST	chr6:87863843-87867122	H1-neurons	neurons:	n/a	chr6:87865663-87865673 chr6:87866037-87866050 chr6:87864645-87864659 chr6:87865958-87865967

No.	Distal block	Cell Line	Cell type
1	chr6:87862757..87864268-chr6:87915198..87917415,2	MCF-7	breast:
2	chr6:87860967..87863617-chr6:87863794..87865835,2	K562	blood:
3	chr6:86386962..86389714-chr6:87862273..87864563,2	MCF-7	breast:
4	chr6:87863665..87867000-chr6:88180798..88183159,3	K562	blood:
5	chr6:87863356..87867363-chr6:87942975..87946448,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CGA-2	chr6:87860877-87865003	ENSG00000272008.1

Variant related genes	Relation type
ZNF292	TF binding region
ENSG00000203875	Chromatin interaction
ENSG00000164414	Chromatin interaction
ENSG00000188994	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13194868	0.82[AFR][1000 genomes]
rs1328477	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1610330	0.81[EUR][1000 genomes]
rs2240461	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2875533	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4706290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4707349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7773715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9294366	0.91[CEU][hapmap]
rs932742	0.90[CEU][hapmap]
rs9444485	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444489	1.00[YRI][hapmap]
rs9450629	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450654	1.00[YRI][hapmap]
rs9450655	1.00[YRI][hapmap]
rs9450659	1.00[JPT][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	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv604114	chr6:87816905-87906053	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9450624	ENSG00000188994	cis	multi-tissue	Pritchard
rs9450624	Hs.485895	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87861000-87866200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:87861200-87866600	Active TSS	Aorta	Aorta
3	chr6:87861200-87866600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr6:87862000-87864400	Flanking Active TSS	Fetal Brain Male	brain
5	chr6:87862200-87864200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:87862200-87864200	Enhancers	Fetal Heart	heart
7	chr6:87862200-87865000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:87862400-87864400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:87862400-87864400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr6:87862400-87864400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:87862400-87864400	Weak transcription	Stomach Mucosa	stomach
12	chr6:87862400-87864600	Weak transcription	Spleen	Spleen
13	chr6:87862600-87864200	Enhancers	Primary T cells from cord blood	blood
14	chr6:87862600-87864200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr6:87862600-87864200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:87862600-87864200	Weak transcription	Placenta	Placenta
17	chr6:87862600-87864200	Weak transcription	HSMM	muscle
18	chr6:87862600-87864400	Weak transcription	Colonic Mucosa	Colon
19	chr6:87862600-87864400	Weak transcription	Esophagus	oesophagus
20	chr6:87862600-87864400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:87862600-87864400	Weak transcription	Left Ventricle	heart
22	chr6:87862600-87864400	Weak transcription	Ovary	ovary
23	chr6:87862600-87864400	Weak transcription	Pancreas	Pancrea
24	chr6:87862600-87864400	Weak transcription	Right Ventricle	heart
25	chr6:87862600-87864600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:87862600-87864600	Weak transcription	Gastric	stomach
27	chr6:87862600-87864600	Weak transcription	Lung	lung
28	chr6:87862600-87864600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:87862600-87867400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:87862800-87864200	Enhancers	Primary hematopoietic stem cells	blood
31	chr6:87862800-87864200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:87862800-87864200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:87862800-87864200	Enhancers	Colon Smooth Muscle	Colon
34	chr6:87862800-87864200	Enhancers	Fetal Kidney	kidney
35	chr6:87862800-87864200	Enhancers	Fetal Stomach	stomach
36	chr6:87862800-87864200	Weak transcription	Psoas Muscle	Psoas
37	chr6:87862800-87864400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr6:87862800-87864400	Enhancers	Primary B cells from peripheral blood	blood
39	chr6:87862800-87864400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:87863000-87864200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr6:87863000-87864200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr6:87863000-87864200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:87863000-87864200	Enhancers	Brain Hippocampus Middle	brain
44	chr6:87863200-87864200	Enhancers	Primary B cells from cord blood	blood
45	chr6:87863200-87864200	Enhancers	Liver	Liver
46	chr6:87863200-87864200	Enhancers	Brain Substantia Nigra	brain
47	chr6:87863200-87864200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr6:87863200-87864200	Enhancers	Hela-S3	cervix
49	chr6:87863200-87864400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr6:87863200-87864400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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