Variant report

Variant	rs2744971
Chromosome Location	chr6:34581636-34581637
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:34204068..34206001-chr6:34581430..34584116,2	K562	blood:
2	chr6:34393119..34395075-chr6:34580866..34582644,2	K562	blood:

Variant related genes	Relation type
ENSG00000137309	Chromatin interaction
ENSG00000270800	Chromatin interaction
ENSG00000124614	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11752260	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092344	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252551	0.81[YRI][hapmap]
rs2492859	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492863	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744937	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]
rs2744938	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2744939	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744942	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[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	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744955	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744956	1.00[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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744965	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744972	1.00[CEU][hapmap];1.00[JPT][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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764205	1.00[CEU][hapmap]
rs2814943	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814944	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2814948	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2814973	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814977	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814983	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814985	1.00[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]
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[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814996	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815003	0.81[YRI][hapmap]
rs2815005	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800457	1.00[CEU][hapmap];1.00[JPT][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	1.00[CEU][hapmap]
rs9469864	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
8	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
9	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
10	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
11	nsv885794	chr6:34561585-34673149	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer 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	42 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	23563607	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2744971	C6orf107	Cis_1M	lymphoblastoid	RTeQTL
rs2744971	C6orf106	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34556200-34612200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:34557400-34612400	Weak transcription	Fetal Kidney	kidney
3	chr6:34562600-34585200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:34567000-34612200	Weak transcription	Fetal Lung	lung
5	chr6:34567800-34612400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:34569400-34583600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:34570400-34612600	Weak transcription	Brain Anterior Caudate	brain
8	chr6:34570600-34583600	Weak transcription	HSMMtube	muscle
9	chr6:34570600-34610000	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:34570800-34581800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:34570800-34582000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:34570800-34584600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:34570800-34587000	Weak transcription	Brain Substantia Nigra	brain
14	chr6:34570800-34618800	Weak transcription	Brain Angular Gyrus	brain
15	chr6:34571000-34585200	Weak transcription	Right Ventricle	heart
16	chr6:34571000-34621400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:34571000-34624000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:34572400-34612600	Weak transcription	Aorta	Aorta
19	chr6:34573800-34607200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:34574400-34584200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:34574400-34612400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr6:34574400-34623400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:34574600-34583400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:34574600-34583400	Weak transcription	Spleen	Spleen
25	chr6:34574600-34583800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:34574600-34583800	Weak transcription	Thymus	Thymus
27	chr6:34574600-34585200	Weak transcription	Ovary	ovary
28	chr6:34574600-34598200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:34574600-34598200	Weak transcription	Lung	lung
30	chr6:34574600-34612600	Weak transcription	Gastric	stomach
31	chr6:34574600-34613600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:34574600-34613600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:34574800-34581800	Weak transcription	Fetal Intestine Small	intestine
34	chr6:34574800-34583200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:34574800-34583600	Weak transcription	Esophagus	oesophagus
36	chr6:34574800-34583800	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:34574800-34590400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:34574800-34596400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:34574800-34596600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:34574800-34596600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:34574800-34611800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:34574800-34612200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:34574800-34612400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:34574800-34612400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr6:34574800-34612600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:34574800-34613200	Weak transcription	Small Intestine	intestine
47	chr6:34575000-34612400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:34575000-34612400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:34575000-34612600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:34575000-34618800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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