Variant report

Variant	rs6484831
Chromosome Location	chr11:36286244-36286245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:36177041..36178787-chr11:36285024..36287447,2	MCF-7	breast:
2	chr11:35638958..35641103-chr11:36285912..36290081,3	MCF-7	breast:
3	chr11:36279472..36281764-chr11:36285267..36287632,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179431	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11033524	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11033527	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11603166	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12361221	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1562327	0.81[CEU][hapmap]
rs1900336	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2289986	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2289987	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4418777	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56386213	0.81[EUR][1000 genomes]
rs61878683	0.81[EUR][1000 genomes]
rs61878687	0.86[EUR][1000 genomes]
rs7104737	0.85[CHB][hapmap]
rs7107433	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7109505	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72946165	0.81[EUR][1000 genomes]
rs7951298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9667667	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9787880	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9787894	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9888212	0.94[EUR][1000 genomes]
rs9888261	0.96[CEU][hapmap];0.94[EUR][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	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6484831	LINC00610	cis	Thyroid	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36276800-36294400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:36278200-36292600	Weak transcription	Esophagus	oesophagus
3	chr11:36278200-36293200	Weak transcription	Fetal Lung	lung
4	chr11:36279200-36292000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:36279200-36294800	Weak transcription	HMEC	breast
6	chr11:36280000-36287400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:36280400-36287400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:36280400-36287600	Weak transcription	Brain Anterior Caudate	brain
9	chr11:36280400-36287600	Weak transcription	Fetal Brain Female	brain
10	chr11:36280400-36291200	Weak transcription	Brain Angular Gyrus	brain
11	chr11:36280400-36294800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:36280400-36299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:36280800-36291200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:36280800-36291400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:36280800-36292000	Weak transcription	Brain Substantia Nigra	brain
16	chr11:36280800-36300200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:36281000-36287400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:36281000-36292600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:36281400-36292200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:36281400-36293200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:36282000-36287400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:36282000-36292000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr11:36282200-36302000	Weak transcription	NHEK	skin
24	chr11:36282800-36292200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:36283000-36291200	Weak transcription	Spleen	Spleen
26	chr11:36283000-36298000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:36283200-36300000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:36285000-36291000	Weak transcription	Fetal Intestine Small	intestine
29	chr11:36285800-36286400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:36285800-36287000	Bivalent Enhancer	Fetal Muscle Leg	muscle
31	chr11:36286000-36286600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:36286000-36286800	Enhancers	Fetal Muscle Trunk	muscle
33	chr11:36286200-36286400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:36286200-36287600	Enhancers	Cortex derived primary cultured neurospheres	brain

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