Variant report

Variant	rs236285
Chromosome Location	chr1:94132788-94132789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94105482..94107011-chr1:94132272..94133832,2	MCF-7	breast:
2	chr1:94127629..94130462-chr1:94131562..94133836,2	MCF-7	breast:
3	chr1:94130370..94133890-chr1:94136641..94140326,4	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1011903	0.87[CEU][hapmap];0.91[GIH][hapmap]
rs11164963	0.87[CEU][hapmap];0.91[GIH][hapmap]
rs12057736	0.84[ASN][1000 genomes]
rs12059154	0.84[ASN][1000 genomes]
rs12084853	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs12092517	0.85[CEU][hapmap]
rs12568405	0.86[JPT][hapmap]
rs1292929	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1567791	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs236273	0.88[AMR][1000 genomes]
rs236284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236288	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236291	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236292	0.88[ASN][1000 genomes]
rs236301	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236306	0.85[MEX][hapmap]
rs236307	0.85[MEX][hapmap]
rs236308	0.87[YRI][hapmap];0.85[AMR][1000 genomes]
rs236311	0.84[AMR][1000 genomes]
rs236312	0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs368888	0.85[AMR][1000 genomes]
rs423493	0.86[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes]
rs6541387	0.87[CEU][hapmap];0.86[ASN][1000 genomes]
rs6541389	0.87[CEU][hapmap];0.86[ASN][1000 genomes]
rs6656270	0.85[CEU][hapmap]
rs6657709	0.87[CEU][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs6660740	0.87[CEU][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs6684568	0.82[ASN][1000 genomes]
rs6694536	0.84[ASN][1000 genomes]
rs6701871	0.82[ASN][1000 genomes]
rs6702036	0.87[CEU][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs6704479	0.86[CEU][hapmap];0.83[GIH][hapmap]
rs7519952	0.90[ASN][1000 genomes]
rs798213	0.91[YRI][hapmap];0.85[AMR][1000 genomes]
rs955470	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs236285	F3	cis	cerebellum	SCAN
rs236285	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94100000-94135800	Weak transcription	Fetal Stomach	stomach
2	chr1:94103800-94135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:94123200-94135800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:94126200-94134600	Weak transcription	Primary B cells from cord blood	blood
5	chr1:94127000-94133600	Enhancers	Ovary	ovary
6	chr1:94127200-94134000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr1:94127400-94132800	Enhancers	Brain Anterior Caudate	brain
8	chr1:94127400-94133600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:94127400-94143800	Genic enhancers	HMEC	breast
10	chr1:94127400-94144000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:94127800-94134000	Enhancers	Colon Smooth Muscle	Colon
12	chr1:94128400-94134200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:94128800-94134000	Enhancers	Right Atrium	heart
14	chr1:94128800-94137800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:94129000-94137000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:94129200-94144800	Weak transcription	GM12878-XiMat	blood
17	chr1:94129400-94137600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:94129600-94133400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:94129800-94135000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:94130200-94132800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:94130200-94133400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:94130400-94134000	Enhancers	Esophagus	oesophagus
23	chr1:94130600-94134400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:94130800-94133000	Weak transcription	Stomach Mucosa	stomach
25	chr1:94130800-94134600	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:94130800-94134800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:94130800-94141000	Genic enhancers	HSMM	muscle
28	chr1:94131000-94134600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:94131000-94138000	Weak transcription	Fetal Brain Male	brain
30	chr1:94131200-94133200	Weak transcription	Fetal Intestine Large	intestine
31	chr1:94131200-94133400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:94131200-94134600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:94131200-94134600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:94131200-94134600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:94131200-94134800	Genic enhancers	HUVEC	blood vessel
36	chr1:94131200-94136200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:94131200-94136200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:94131200-94144000	Genic enhancers	Placenta	Placenta
39	chr1:94131400-94132800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr1:94131400-94134200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:94131400-94135800	Weak transcription	Aorta	Aorta
42	chr1:94131400-94136400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:94131400-94137000	Genic enhancers	A549	lung
44	chr1:94131400-94140600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:94131600-94133200	Genic enhancers	Psoas Muscle	Psoas
46	chr1:94131600-94134600	Weak transcription	Brain Angular Gyrus	brain
47	chr1:94131600-94136200	Weak transcription	Fetal Lung	lung
48	chr1:94131600-94143800	Genic enhancers	NHEK	skin
49	chr1:94131800-94132800	Genic enhancers	Osteobl	bone
50	chr1:94131800-94133400	Enhancers	HUES64 Cell Line	embryonic stem cell

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