Variant report

Variant	rs13217234
Chromosome Location	chr6:38608869-38608870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:38606851-38609084	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:38608726-38608926	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:38565254..38567561-chr6:38606168..38608897,2	MCF-7	breast:
2	chr6:38606797..38609056-chr6:38670128..38671908,2	K562	blood:
3	chr6:38605277..38607230-chr6:38608690..38610298,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNAH8-8	chr6:38607926-38617146	NONHSAT112318

No data

Variant related genes	Relation type
BTBD9	TF binding region
ENSG00000183826	Chromatin interaction
ENSG00000124767	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10484855	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1130534	0.80[EUR][1000 genomes]
rs11751782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206711	1.00[ASN][1000 genomes]
rs12212784	1.00[ASN][1000 genomes]
rs12524122	1.00[YRI][hapmap]
rs12526818	1.00[YRI][hapmap]
rs12528446	1.00[YRI][hapmap]
rs13191302	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194237	0.85[EUR][1000 genomes]
rs13196530	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196708	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198900	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13199033	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202862	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203443	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209846	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210334	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212218	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213257	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214969	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13215896	0.88[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13218305	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219252	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219395	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13219781	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1698998	1.00[ASN][1000 genomes]
rs17544311	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17544868	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17614684	0.88[CEU][hapmap]
rs1937782	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2654449	1.00[ASN][1000 genomes]
rs28360530	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34349982	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34360712	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34408317	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34470929	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34519749	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34637217	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34695044	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34897279	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34962226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34971977	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35147121	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35152718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35207097	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35266471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35364976	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35388596	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35901431	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35975219	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67457665	1.00[ASN][1000 genomes]
rs6932648	0.88[CEU][hapmap]
rs71544423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571331	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72856580	1.00[ASN][1000 genomes]
rs73416349	1.00[ASN][1000 genomes]
rs73416350	1.00[ASN][1000 genomes]
rs73416351	1.00[ASN][1000 genomes]
rs7451595	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7604	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746400	1.00[ASN][1000 genomes]
rs7750789	1.00[ASN][1000 genomes]
rs7762397	1.00[ASN][1000 genomes]
rs9394523	0.88[CEU][hapmap]
rs9394524	0.88[CEU][hapmap]
rs963720	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38606200-38609000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:38606600-38609000	Active TSS	Lung	lung
3	chr6:38607800-38609000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr6:38607800-38609200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:38608000-38609000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:38608000-38609000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:38608000-38609000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr6:38608000-38609000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr6:38608000-38609000	Flanking Active TSS	Colonic Mucosa	Colon
10	chr6:38608000-38609000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr6:38608000-38609000	Flanking Active TSS	Dnd41	blood
12	chr6:38608000-38609000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr6:38608200-38609000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr6:38608200-38609000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:38608200-38609000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr6:38608200-38609000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:38608200-38609000	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr6:38608200-38609000	Flanking Active TSS	Fetal Brain Female	brain
19	chr6:38608200-38609000	Flanking Active TSS	Fetal Lung	lung
20	chr6:38608200-38609000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr6:38608200-38609000	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr6:38608200-38609000	Enhancers	Spleen	Spleen
23	chr6:38608200-38609000	Flanking Active TSS	HUVEC	blood vessel
24	chr6:38608200-38609200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:38608200-38609200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr6:38608400-38609000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:38608400-38609000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:38608400-38609000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr6:38608400-38609000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:38608400-38609000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:38608400-38609000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr6:38608400-38609000	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr6:38608400-38609000	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr6:38608400-38609000	Flanking Active TSS	Left Ventricle	heart
35	chr6:38608400-38609000	Flanking Active TSS	Osteobl	bone
36	chr6:38608400-38609200	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr6:38608400-38609200	Flanking Active TSS	NHLF	lung
38	chr6:38608400-38609400	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr6:38608600-38609000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:38608600-38609000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr6:38608600-38609000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:38608600-38609000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:38608600-38609000	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr6:38608600-38609000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr6:38608600-38609000	Enhancers	Esophagus	oesophagus
46	chr6:38608600-38609000	Enhancers	Fetal Thymus	thymus
47	chr6:38608600-38609000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr6:38608600-38609000	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr6:38608600-38609000	Flanking Active TSS	GM12878-XiMat	blood
50	chr6:38608600-38609200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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