Variant report

Variant	rs7756284
Chromosome Location	chr6:110083056-110083057
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	chr6:110011565..110014032-chr6:110081170..110083207,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112367	Chromatin interaction
ENSG00000155085	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1096136	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs11751112	0.96[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753828	0.85[CEU][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754263	0.84[CEU][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11757485	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11757580	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11759958	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17540056	0.82[CEU][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17612758	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17612996	0.96[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947004	0.82[CEU][hapmap];0.80[YRI][hapmap]
rs4947006	0.82[CEU][hapmap];0.82[YRI][hapmap]
rs56009458	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125306	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56264193	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58068940	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437563	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437568	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568583	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs6568591	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs6568601	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568604	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900133	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6900187	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6917300	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6921303	0.82[CEU][hapmap];0.83[YRI][hapmap]
rs6924436	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931630	0.82[CEU][hapmap]
rs6942171	0.81[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772938	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs911022	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs911023	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs9320303	0.82[CEU][hapmap]
rs9372220	0.81[CEU][hapmap];0.86[YRI][hapmap]
rs9374121	0.81[CEU][hapmap];0.86[EUR][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	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv5436	chr6:110052812-110097662	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv886533	chr6:110067773-110126393	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7756284	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
2	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
3	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
5	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
6	chr6:110042200-110088800	Weak transcription	Fetal Intestine Small	intestine
7	chr6:110042400-110089000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
9	chr6:110047200-110084000	Weak transcription	Small Intestine	intestine
10	chr6:110048600-110089800	Weak transcription	Fetal Kidney	kidney
11	chr6:110057200-110089000	Weak transcription	Fetal Brain Female	brain
12	chr6:110057400-110089000	Weak transcription	Esophagus	oesophagus
13	chr6:110057600-110086200	Weak transcription	Brain Anterior Caudate	brain
14	chr6:110058200-110087200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:110058200-110089000	Weak transcription	Lung	lung
16	chr6:110058400-110085000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:110058400-110089600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:110058800-110112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:110059200-110124000	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:110060000-110087800	Weak transcription	Fetal Thymus	thymus
21	chr6:110061200-110089200	Weak transcription	Pancreas	Pancrea
22	chr6:110062600-110089200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:110062800-110087400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:110062800-110088000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:110065200-110084000	Weak transcription	Left Ventricle	heart
26	chr6:110065200-110089000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:110065200-110111200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:110065400-110094200	Weak transcription	Brain Substantia Nigra	brain
29	chr6:110065600-110084000	Weak transcription	Placenta	Placenta
30	chr6:110065600-110087200	Weak transcription	HSMMtube	muscle
31	chr6:110065600-110087400	Weak transcription	Fetal Stomach	stomach
32	chr6:110065600-110089000	Weak transcription	Gastric	stomach
33	chr6:110065600-110089200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:110065800-110086200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:110065800-110086400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:110065800-110087200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr6:110065800-110087200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:110065800-110088600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:110065800-110089000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:110065800-110089000	Weak transcription	Brain Hippocampus Middle	brain
41	chr6:110065800-110089000	Weak transcription	Thymus	Thymus
42	chr6:110065800-110107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:110065800-110107400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:110066000-110087200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:110067800-110089000	Weak transcription	Fetal Lung	lung
46	chr6:110068000-110083200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr6:110069400-110086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:110069800-110089200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:110070000-110084000	Weak transcription	Primary T cells from cord blood	blood
50	chr6:110070200-110087200	Weak transcription	Adipose Nuclei	Adipose

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