Variant report

Variant	rs2744937
Chromosome Location	chr6:34557246-34557247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34494734..34495415-chr6:34557190..34557693,2	MCF-7	breast:
2	chr6:34479843..34482340-chr6:34557175..34560153,2	K562	blood:
3	chr6:34497199..34497799-chr6:34557125..34558123,2	MCF-7	breast:
4	chr6:34556477..34558715-chr6:34566152..34568082,2	K562	blood:
5	chr6:34497355..34498033-chr6:34557195..34557723,2	MCF-7	breast:
6	chr6:34551284..34553223-chr6:34555958..34557670,2	MCF-7	breast:
7	chr6:34555563..34557937-chr6:34565420..34567500,2	MCF-7	breast:
8	chr6:34543365..34546387-chr6:34554474..34557693,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196114	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11752260	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092344	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252551	0.81[YRI][hapmap]
rs2492859	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492863	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744938	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2744939	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744942	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744947	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744954	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744955	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744956	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744963	0.81[YRI][hapmap]
rs2744964	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744965	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744966	0.81[YRI][hapmap]
rs2744971	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744972	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744977	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764205	0.90[CEU][hapmap]
rs2814943	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814944	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2814948	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2814950	0.81[YRI][hapmap]
rs2814973	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814977	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814986	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814990	0.81[YRI][hapmap]
rs2814993	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814994	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814996	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814998	0.81[YRI][hapmap]
rs2815003	0.81[YRI][hapmap]
rs2815005	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800457	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800461	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56930444	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907508	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938239	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462007	0.90[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs9462014	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs9469864	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv516578	chr6:34483015-34561585	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv885792	chr6:34507311-34607958	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv823667	chr6:34533015-34592524	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv818410	chr6:34538544-34579431	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2744937	C6orf107	Cis_1M	lymphoblastoid	RTeQTL
rs2744937	C6orf106	cis	parietal	SCAN
rs2744937	C6orf106	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34535600-34563200	Weak transcription	A549	lung
2	chr6:34546000-34559800	Weak transcription	HSMM	muscle
3	chr6:34547200-34566800	Weak transcription	Aorta	Aorta
4	chr6:34548800-34561400	Weak transcription	Fetal Heart	heart
5	chr6:34549000-34564200	Strong transcription	Fetal Intestine Small	intestine
6	chr6:34549400-34559800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:34549400-34564400	Weak transcription	Brain Substantia Nigra	brain
8	chr6:34549800-34564200	Strong transcription	Fetal Stomach	stomach
9	chr6:34551400-34559000	Strong transcription	Primary T cells from cord blood	blood
10	chr6:34552600-34558400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:34552800-34558000	Strong transcription	Fetal Intestine Large	intestine
12	chr6:34553000-34558200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:34553000-34558800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr6:34553000-34559600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:34553200-34558600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr6:34553200-34558600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:34553200-34558800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr6:34553200-34559000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:34553400-34558800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr6:34553400-34559200	Strong transcription	HepG2	liver
21	chr6:34553400-34562200	Weak transcription	Small Intestine	intestine
22	chr6:34553400-34570000	Weak transcription	NH-A	brain
23	chr6:34553600-34558400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:34553600-34558400	Strong transcription	Thymus	Thymus
25	chr6:34553600-34559600	Weak transcription	Brain Anterior Caudate	brain
26	chr6:34553600-34559600	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:34553600-34566400	Weak transcription	Brain Germinal Matrix	brain
28	chr6:34553800-34558200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:34553800-34558400	Strong transcription	Lung	lung
30	chr6:34553800-34558600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:34553800-34558600	Strong transcription	Fetal Muscle Leg	muscle
32	chr6:34553800-34558800	Strong transcription	Liver	Liver
33	chr6:34553800-34562800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:34554000-34557600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr6:34554000-34557600	Strong transcription	Spleen	Spleen
36	chr6:34554000-34557800	Strong transcription	Fetal Thymus	thymus
37	chr6:34554000-34558400	Weak transcription	Fetal Brain Female	brain
38	chr6:34554000-34573600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:34554200-34557800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr6:34554200-34558000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:34554200-34558400	Weak transcription	Psoas Muscle	Psoas
42	chr6:34554200-34558600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:34554200-34558600	Strong transcription	Dnd41	blood
44	chr6:34554200-34558800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:34554200-34559000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr6:34554200-34559800	Weak transcription	Brain Angular Gyrus	brain
47	chr6:34554200-34559800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:34554200-34563000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:34554400-34558000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:34554400-34558600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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