Variant report

Variant	rs3115668
Chromosome Location	chr6:31641485-31641486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:31640888..31643598-chr6:31665920..31668358,2	MCF-7	breast:
2	chr6:31588850..31591335-chr6:31641396..31643274,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LY6G5B-1	chr6:31640938-31641553	NONHSAT108816

Variant related genes	Relation type
ENSG00000200816	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2736177	0.81[EUR][1000 genomes]
rs2857594	0.84[EUR][1000 genomes]
rs2857600	0.81[EUR][1000 genomes]
rs2857609	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3115669	0.83[EUR][1000 genomes]
rs3117578	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130050	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130068	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130071	0.80[EUR][1000 genomes]
rs3130625	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131376	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131377	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
15	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3115668	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31634800-31648200	Weak transcription	Right Atrium	heart
2	chr6:31635000-31641800	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:31635000-31641800	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr6:31635000-31642000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:31635000-31642000	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:31635000-31642000	Strong transcription	Brain Inferior Temporal Lobe	brain
7	chr6:31635000-31642000	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:31635000-31642000	Strong transcription	Spleen	Spleen
9	chr6:31635000-31642200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr6:31635000-31642800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:31635000-31642800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:31635000-31643800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:31635200-31641600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:31635200-31641800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:31635200-31641800	Strong transcription	HSMMtube	muscle
16	chr6:31635200-31642000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:31635200-31642200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:31635200-31643600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr6:31635400-31641600	Strong transcription	Fetal Brain Female	brain
20	chr6:31635400-31642000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:31635400-31642000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:31635400-31642000	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr6:31635400-31642000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:31635400-31642000	Strong transcription	Fetal Intestine Large	intestine
25	chr6:31635400-31642000	Strong transcription	HSMM	muscle
26	chr6:31635400-31643000	Strong transcription	Fetal Muscle Leg	muscle
27	chr6:31635400-31643000	Strong transcription	Lung	lung
28	chr6:31635400-31643600	Strong transcription	Primary T cells from cord blood	blood
29	chr6:31635400-31643600	Strong transcription	Brain Anterior Caudate	brain
30	chr6:31635600-31641600	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr6:31635600-31641800	Strong transcription	NH-A	brain
32	chr6:31635600-31642000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:31635600-31642000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:31635600-31642000	Strong transcription	Brain Substantia Nigra	brain
35	chr6:31635600-31642000	Strong transcription	Gastric	stomach
36	chr6:31635600-31642000	Strong transcription	Osteobl	bone
37	chr6:31635600-31642200	Strong transcription	Rectal Smooth Muscle	rectum
38	chr6:31635600-31643800	Strong transcription	Thymus	Thymus
39	chr6:31635600-31644600	Strong transcription	Fetal Intestine Small	intestine
40	chr6:31635600-31644600	Strong transcription	Fetal Stomach	stomach
41	chr6:31635800-31641800	Strong transcription	Brain Hippocampus Middle	brain
42	chr6:31635800-31642000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:31635800-31642000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:31635800-31642000	Strong transcription	Placenta	Placenta
45	chr6:31635800-31642000	Strong transcription	NHEK	skin
46	chr6:31635800-31642800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:31636000-31641800	Strong transcription	Pancreas	Pancrea
48	chr6:31636000-31642000	Strong transcription	Colon Smooth Muscle	Colon
49	chr6:31636000-31642200	Strong transcription	Liver	Liver
50	chr6:31636000-31648400	Weak transcription	Fetal Heart	heart

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