Variant report

Variant	rs10946197
Chromosome Location	chr6:167348416-167348417
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:167343672-167349201	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:167334630..167336985-chr6:167348242..167350494,2	K562	blood:
2	chr6:167344148..167347113-chr6:167348259..167349932,2	K562	blood:
3	chr6:167320098..167322424-chr6:167348297..167350309,2	K562	blood:
4	chr6:167347041..167349963-chr6:167389073..167391060,2	K562	blood:
5	chr6:167339433..167341286-chr6:167346948..167348863,2	K562	blood:
6	chr6:167344148..167347081-chr6:167347085..167349759,2	K562	blood:

No data

Variant related genes	Relation type
RNASET2	TF binding region
ENSG00000026297	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12203820	1.00[ASN][1000 genomes]
rs12205779	1.00[ASN][1000 genomes]
rs13213697	1.00[CHB][hapmap]
rs13220568	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55843050	1.00[ASN][1000 genomes]
rs62436419	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62436761	1.00[ASN][1000 genomes]
rs62438869	1.00[ASN][1000 genomes]
rs71571466	1.00[ASN][1000 genomes]
rs9457237	1.00[ASN][1000 genomes]
rs9457243	1.00[ASN][1000 genomes]
rs9459809	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv605327	chr6:167185674-167360389	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1027314	chr6:167194653-167355961	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv538542	chr6:167194653-167355961	Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv605332	chr6:167198027-167353701	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
9	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
12	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10946197	AL133458.1	cis	Whole Blood	GTEx
rs10946197	CCR6	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167337600-167350000	Weak transcription	Ovary	ovary
2	chr6:167337600-167363400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:167338200-167356000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:167340000-167358800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:167340000-167363000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr6:167340000-167363000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:167340200-167349800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:167340200-167354600	Strong transcription	Fetal Intestine Small	intestine
9	chr6:167340200-167362800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr6:167340400-167357200	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:167340400-167363000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:167340600-167353400	Strong transcription	HepG2	liver
13	chr6:167340600-167363000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:167340800-167350000	Weak transcription	Fetal Brain Female	brain
15	chr6:167340800-167359600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:167341000-167349800	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:167341000-167368800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:167341200-167348800	Strong transcription	Thymus	Thymus
19	chr6:167341200-167368800	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:167341400-167361400	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr6:167341600-167351200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:167342000-167351200	Weak transcription	Small Intestine	intestine
23	chr6:167342200-167348600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:167342200-167354000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:167342400-167351200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:167342400-167359600	Weak transcription	Placenta	Placenta
27	chr6:167342400-167368600	Weak transcription	Fetal Heart	heart
28	chr6:167342800-167351600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:167343200-167351200	Weak transcription	Brain Germinal Matrix	brain
30	chr6:167343600-167352800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:167343800-167349800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:167343800-167351200	Weak transcription	Stomach Mucosa	stomach
33	chr6:167343800-167354600	Strong transcription	Fetal Stomach	stomach
34	chr6:167344000-167350000	Strong transcription	Primary B cells from cord blood	blood
35	chr6:167344000-167351600	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:167344200-167353000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:167344200-167364000	Weak transcription	Brain Angular Gyrus	brain
38	chr6:167344200-167368600	Weak transcription	Right Atrium	heart
39	chr6:167344400-167349200	Strong transcription	Spleen	Spleen
40	chr6:167344400-167349800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:167344400-167351000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:167344400-167351200	Weak transcription	Brain Anterior Caudate	brain
43	chr6:167344400-167351200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:167344400-167351400	Weak transcription	Fetal Kidney	kidney
45	chr6:167344400-167351800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:167344400-167358200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr6:167344400-167362000	Strong transcription	GM12878-XiMat	blood
48	chr6:167344400-167363600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:167344400-167364000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:167344600-167351200	Weak transcription	K562	blood

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