Variant report

Variant	rs4326407
Chromosome Location	chr8:118838952-118838953
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	chr8:118836744..118839652-chr8:118842920..118845860,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11546829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11778143	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11780721	1.00[JPT][hapmap]
rs17430126	0.90[CEU][hapmap]
rs17430133	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17430224	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17430245	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17439659	0.90[CEU][hapmap]
rs4366105	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4463453	0.82[ASW][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap]
rs4531086	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4546690	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4876393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4876758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4876759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4876761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469711	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7005512	0.90[CEU][hapmap]
rs7009420	0.90[CEU][hapmap]
rs7820199	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[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	nsv1019636	chr8:118598433-118946091	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv539734	chr8:118598433-118946091	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831439	chr8:118747352-118899118	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv933516	chr8:118764605-119009093	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4326407	EXT1	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118801000-118843600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr8:118805600-118849800	Strong transcription	Liver	Liver
3	chr8:118808600-118849400	Weak transcription	Stomach Mucosa	stomach
4	chr8:118810000-118843800	Weak transcription	Fetal Heart	heart
5	chr8:118814000-118842200	Weak transcription	Primary B cells from cord blood	blood
6	chr8:118817200-118852400	Weak transcription	Psoas Muscle	Psoas
7	chr8:118817200-118852400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr8:118819000-118842000	Weak transcription	Fetal Kidney	kidney
9	chr8:118819600-118851000	Weak transcription	Fetal Thymus	thymus
10	chr8:118825000-118844800	Weak transcription	Brain Germinal Matrix	brain
11	chr8:118825000-118850000	Weak transcription	Fetal Brain Female	brain
12	chr8:118825200-118841000	Weak transcription	Thymus	Thymus
13	chr8:118825200-118848000	Weak transcription	Colonic Mucosa	Colon
14	chr8:118825200-118859600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:118825200-118859800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr8:118825400-118849200	Weak transcription	Brain Hippocampus Middle	brain
17	chr8:118825400-118849600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:118825400-118852400	Weak transcription	Right Ventricle	heart
19	chr8:118825400-118853200	Weak transcription	Brain Anterior Caudate	brain
20	chr8:118825400-118859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr8:118825600-118843800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr8:118825600-118849600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr8:118825600-118849800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr8:118825600-118857200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr8:118825600-118860000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr8:118825800-118846400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr8:118825800-118850400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr8:118827200-118847200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr8:118827200-118855000	Weak transcription	Right Atrium	heart
30	chr8:118827600-118841200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr8:118827800-118841000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr8:118827800-118844000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr8:118828600-118857000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr8:118828800-118841000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr8:118829200-118847800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr8:118829800-118855000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr8:118829800-118859800	Weak transcription	Esophagus	oesophagus
38	chr8:118830600-118841000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr8:118830800-118843400	Weak transcription	HSMMtube	muscle
40	chr8:118831200-118846200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr8:118832200-118854800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr8:118832400-118854000	Weak transcription	Gastric	stomach
43	chr8:118832400-118855000	Weak transcription	Colon Smooth Muscle	Colon
44	chr8:118832600-118840800	Weak transcription	Aorta	Aorta
45	chr8:118832600-118842200	Weak transcription	Dnd41	blood
46	chr8:118832600-118854400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr8:118832600-118855000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr8:118832600-118859800	Weak transcription	Spleen	Spleen
49	chr8:118832800-118840600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr8:118832800-118841000	Weak transcription	Ovary	ovary

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