Variant report

Variant	rs3846842
Chromosome Location	chr6:26423591-26423592
allele	C/G
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	RFX5	chr6:26419671-26423665	IMR90	lung:	n/a	chr6:26421550-26421558
2	RFX5	chr6:26419605-26423677	SK-N-SH	brain:	n/a	chr6:26421550-26421558

Variant related genes	Relation type
BTN2A3P	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1131936	1.00[JPT][hapmap]
rs11963680	1.00[ASN][1000 genomes]
rs11966630	0.89[ASN][1000 genomes]
rs12208788	1.00[JPT][hapmap]
rs13437008	1.00[ASN][1000 genomes]
rs13437012	1.00[ASN][1000 genomes]
rs13437351	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13978	1.00[JPT][hapmap]
rs16891666	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1804836	0.89[ASN][1000 genomes]
rs2281027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393650	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3734541	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3757140	0.89[YRI][hapmap]
rs3757141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3757147	0.85[JPT][hapmap]
rs3757149	0.93[YRI][hapmap]
rs3846841	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3857549	1.00[JPT][hapmap]
rs3885849	0.89[ASN][1000 genomes]
rs4422619	1.00[ASN][1000 genomes]
rs4476815	0.85[JPT][hapmap]
rs4712986	1.00[JPT][hapmap]
rs4712988	0.89[ASN][1000 genomes]
rs58380352	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59121933	0.89[ASN][1000 genomes]
rs59621581	0.96[ASN][1000 genomes]
rs6456720	1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6456725	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6456726	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6456730	1.00[ASN][1000 genomes]
rs6901118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6907857	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6910849	1.00[JPT][hapmap]
rs6910871	1.00[JPT][hapmap]
rs6910921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6910993	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6911470	1.00[JPT][hapmap]
rs6911476	1.00[JPT][hapmap]
rs6929846	1.00[JPT][hapmap]
rs6935678	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6941018	1.00[ASN][1000 genomes]
rs72500814	0.89[ASN][1000 genomes]
rs7355	1.00[JPT][hapmap]
rs7356849	1.00[JPT][hapmap]
rs7356980	0.89[ASN][1000 genomes]
rs7356982	0.85[JPT][hapmap]
rs7751645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769926	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7773913	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9104	1.00[JPT][hapmap]
rs9295692	1.00[JPT][hapmap]
rs9461247	0.89[ASN][1000 genomes]
rs9461249	0.93[YRI][hapmap]
rs9461252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461253	1.00[JPT][hapmap]
rs9461254	1.00[JPT][hapmap]
rs9461256	1.00[ASN][1000 genomes]
rs9467748	0.85[JPT][hapmap]
rs9467749	0.89[ASN][1000 genomes]
rs9467753	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs9467755	0.89[ASN][1000 genomes]
rs9467756	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467759	1.00[JPT][hapmap]
rs9467760	0.85[JPT][hapmap]
rs9467761	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9467765	1.00[ASN][1000 genomes]
rs9467768	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9467769	1.00[ASN][1000 genomes]
rs9467771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9467788	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9467803	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer 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	1201 gene(s)	inside rSNPs	diseases
4	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription 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	45 gene(s)	inside rSNPs	diseases
5	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv883492	chr6:26367689-26436592	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv883493	chr6:26367689-26442786	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv883494	chr6:26367833-26442786	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv883495	chr6:26367833-26443853	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	esv3334611	chr6:26367893-26443308	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
12	nsv883497	chr6:26369549-26442786	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv883498	chr6:26369549-26443853	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv883499	chr6:26377591-26454454	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription 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	28 gene(s)	inside rSNPs	diseases
15	esv3427999	chr6:26378373-26453532	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
16	nsv462664	chr6:26379537-26451553	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv601184	chr6:26379537-26451553	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26422200-26423600	Weak transcription	Aorta	Aorta
2	chr6:26422200-26424800	Enhancers	Spleen	Spleen
3	chr6:26422200-26425800	Enhancers	Small Intestine	intestine
4	chr6:26422200-26426400	Weak transcription	Placenta	Placenta
5	chr6:26422200-26428400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:26422200-26439800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:26422400-26426400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:26422400-26431000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:26422400-26432000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:26422400-26439400	Weak transcription	Primary T cells from cord blood	blood
11	chr6:26422400-26439400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:26422400-26439600	Weak transcription	Thymus	Thymus
13	chr6:26422600-26423600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:26422600-26423600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:26422600-26423600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr6:26422600-26423600	Enhancers	NHDF-Ad	bronchial
17	chr6:26422600-26423800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:26422600-26423800	Enhancers	Colon Smooth Muscle	Colon
19	chr6:26422600-26423800	Enhancers	Right Atrium	heart
20	chr6:26422600-26423800	Enhancers	K562	blood
21	chr6:26422600-26424600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:26422600-26424800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:26422600-26424800	Enhancers	Duodenum Mucosa	Duodenum
24	chr6:26422600-26424800	Enhancers	Esophagus	oesophagus
25	chr6:26422600-26424800	Genic enhancers	Fetal Stomach	stomach
26	chr6:26422600-26425000	Genic enhancers	Fetal Muscle Leg	muscle
27	chr6:26422600-26426000	Enhancers	Adipose Nuclei	Adipose
28	chr6:26422600-26426200	Weak transcription	Liver	Liver
29	chr6:26422600-26426200	Weak transcription	NH-A	brain
30	chr6:26422600-26426400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:26422600-26426600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:26422600-26426600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:26422600-26426600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:26422600-26426600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr6:26422600-26427000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:26422600-26427400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:26422600-26428200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:26422600-26430800	Weak transcription	A549	lung
39	chr6:26422600-26431000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr6:26422600-26431000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:26422600-26431000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:26422600-26431200	Weak transcription	Fetal Thymus	thymus
43	chr6:26422600-26431400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr6:26422600-26432600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:26422600-26432800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:26422600-26434200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr6:26422600-26434400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:26422600-26434600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:26422600-26439400	Weak transcription	HMEC	breast
50	chr6:26422600-26439600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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