Variant report

Variant	rs9640466
Chromosome Location	chr7:140096175-140096176
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140085401..140088225-chr7:140094986..140096500,2	MCF-7	breast:
2	chr7:140096106..140096834-chr7:140692307..140693078,2	MCF-7	breast:
3	chr7:140009929..140010746-chr7:140096072..140096776,2	MCF-7	breast:
4	chr7:140009842..140010440-chr7:140096015..140096525,2	MCF-7	breast:
5	chr7:140091825..140093719-chr7:140095231..140098227,2	MCF-7	breast:
6	chr7:140009860..140010445-chr7:140095992..140096644,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202472	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10251020	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10256523	0.82[TSI][hapmap]
rs10261444	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10273430	0.87[EUR][1000 genomes]
rs12703828	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13229539	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13235719	0.90[EUR][1000 genomes]
rs13236204	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13246775	0.90[EUR][1000 genomes]
rs62490400	0.90[EUR][1000 genomes]
rs67151693	0.87[EUR][1000 genomes]
rs6954902	0.86[TSI][hapmap]
rs6970119	0.81[CEU][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6978505	0.81[CEU][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv522190	chr7:140066411-140130663	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9640466	ZC3HAV1L	cis	parietal	SCAN
rs9640466	SLC37A3	cis	multi-tissue	Pritchard
rs9640466	OR9A2	cis	cerebellum	SCAN
rs9640466	CREB3L2	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140052000-140097400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:140058800-140097200	Weak transcription	Brain Anterior Caudate	brain
3	chr7:140076800-140096200	Weak transcription	NHLF	lung
4	chr7:140080200-140097200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:140080200-140097200	Weak transcription	HSMMtube	muscle
6	chr7:140080200-140097600	Weak transcription	Brain Angular Gyrus	brain
7	chr7:140080600-140096200	Weak transcription	HepG2	liver
8	chr7:140080600-140097400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:140080800-140096200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:140081400-140097200	Weak transcription	Brain Germinal Matrix	brain
11	chr7:140082200-140096200	Weak transcription	Fetal Lung	lung
12	chr7:140082200-140097000	Weak transcription	Fetal Brain Female	brain
13	chr7:140082200-140097400	Weak transcription	Right Ventricle	heart
14	chr7:140082400-140096400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:140082400-140096600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr7:140082400-140096600	Weak transcription	Fetal Muscle Leg	muscle
17	chr7:140082400-140097000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:140082400-140097200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:140082400-140097200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr7:140082400-140097400	Weak transcription	Fetal Intestine Large	intestine
21	chr7:140082400-140097400	Weak transcription	Ovary	ovary
22	chr7:140086200-140097200	Weak transcription	Psoas Muscle	Psoas
23	chr7:140086800-140097200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:140090400-140096200	Weak transcription	Adipose Nuclei	Adipose
25	chr7:140090400-140097400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:140090800-140096400	Weak transcription	NHDF-Ad	bronchial
27	chr7:140090800-140097400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:140090800-140097600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:140090800-140097600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:140090800-140097600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr7:140090800-140097600	Weak transcription	Spleen	Spleen
32	chr7:140091000-140096200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr7:140091000-140096400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:140091000-140096400	Weak transcription	NH-A	brain
35	chr7:140091000-140097200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:140091000-140097200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:140091000-140097200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr7:140091000-140097200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:140091000-140097400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr7:140091000-140097400	Weak transcription	Thymus	Thymus
41	chr7:140091200-140096400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr7:140091200-140096800	Weak transcription	Fetal Thymus	thymus
43	chr7:140091200-140097200	Weak transcription	HSMM	muscle
44	chr7:140091400-140096200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr7:140091600-140097200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr7:140091800-140097200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr7:140092000-140096200	Weak transcription	Brain Hippocampus Middle	brain
48	chr7:140092000-140096600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:140092000-140097200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr7:140092000-140097200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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