Variant report

Variant	rs11751112
Chromosome Location	chr6:110084078-110084079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:110084003-110084085	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FIG4	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1096136	0.93[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11753828	0.80[CEU][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754263	0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11757485	0.96[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11757580	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11759958	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17540056	0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17612758	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]
rs17612996	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947006	0.82[YRI][hapmap]
rs56009458	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.83[EUR][1000 genomes]
rs58068940	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437563	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437568	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568583	0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs6568591	0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs6568601	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568604	0.92[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	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6921303	0.82[YRI][hapmap]
rs6924436	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6941360	0.83[TSI][hapmap]
rs6942171	1.00[ASW][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756284	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]
rs7772938	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs911022	0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs911023	0.82[YRI][hapmap]
rs9372220	0.86[YRI][hapmap]
rs9374121	0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs9400320	0.81[TSI][hapmap]

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
rs11751112	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
2	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
4	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
5	chr6:110042200-110088800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:110042400-110089000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
8	chr6:110048600-110089800	Weak transcription	Fetal Kidney	kidney
9	chr6:110057200-110089000	Weak transcription	Fetal Brain Female	brain
10	chr6:110057400-110089000	Weak transcription	Esophagus	oesophagus
11	chr6:110057600-110086200	Weak transcription	Brain Anterior Caudate	brain
12	chr6:110058200-110087200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:110058200-110089000	Weak transcription	Lung	lung
14	chr6:110058400-110085000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:110058400-110089600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:110058800-110112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:110059200-110124000	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:110060000-110087800	Weak transcription	Fetal Thymus	thymus
19	chr6:110061200-110089200	Weak transcription	Pancreas	Pancrea
20	chr6:110062600-110089200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:110062800-110087400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:110062800-110088000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:110065200-110089000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:110065200-110111200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:110065400-110094200	Weak transcription	Brain Substantia Nigra	brain
26	chr6:110065600-110087200	Weak transcription	HSMMtube	muscle
27	chr6:110065600-110087400	Weak transcription	Fetal Stomach	stomach
28	chr6:110065600-110089000	Weak transcription	Gastric	stomach
29	chr6:110065600-110089200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:110065800-110086200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:110065800-110086400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:110065800-110087200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr6:110065800-110087200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:110065800-110088600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:110065800-110089000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:110065800-110089000	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:110065800-110089000	Weak transcription	Thymus	Thymus
38	chr6:110065800-110107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:110065800-110107400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:110066000-110087200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:110067800-110089000	Weak transcription	Fetal Lung	lung
42	chr6:110069400-110086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:110069800-110089200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:110070200-110087200	Weak transcription	Adipose Nuclei	Adipose
45	chr6:110070200-110089000	Weak transcription	Aorta	Aorta
46	chr6:110072000-110089000	Weak transcription	Ovary	ovary
47	chr6:110076600-110089000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:110078200-110089000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:110078600-110088000	Weak transcription	NHDF-Ad	bronchial
50	chr6:110078800-110107400	Weak transcription	Fetal Brain Male	brain

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