Variant report

Variant	rs10484441
Chromosome Location	chr6:26474742-26474743
allele	C/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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26474445..26476878-chr6:26512542..26515226,3	K562	blood:
2	chr6:26457588..26459634-chr6:26472542..26475354,3	MCF-7	breast:
3	chr6:26472114..26481394-chr6:26482721..26495847,23	K562	blood:
4	chr6:26474221..26477564-chr6:26521186..26523081,3	K562	blood:
5	chr11:62609018..62609547-chr6:26474168..26475039,2	NB4	blood:
6	chr6:26314124..26316500-chr6:26474166..26476547,2	K562	blood:
7	chr6:26474337..26476257-chr6:26519630..26521866,2	MCF-7	breast:
8	chr6:26156628..26158808-chr6:26474596..26476734,2	MCF-7	breast:
9	chr6:26470620..26472220-chr6:26474706..26477657,2	MCF-7	breast:
10	chr6:26382919..26385188-chr6:26473437..26474979,2	K562	blood:
11	chr6:26342125..26345094-chr6:26474079..26475850,2	K562	blood:
12	chr6:26473312..26475713-chr6:26519494..26521271,2	MCF-7	breast:
13	chr6:26343594..26345212-chr6:26474079..26475915,2	K562	blood:
14	chr6:26474090..26476155-chr6:26476306..26478036,2	MCF-7	breast:
15	chr6:26471319..26475410-chr6:26567164..26571952,5	K562	blood:
16	chr6:26324380..26326185-chr6:26473831..26475753,2	K562	blood:
17	chr6:26472961..26477109-chr6:26519664..26522390,3	K562	blood:
18	chr6:26456009..26458208-chr6:26473841..26475463,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228223	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000124508	Chromatin interaction
ENSG00000199289	Chromatin interaction
ENSG00000112763	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10447390	0.86[CEU][hapmap]
rs10447391	0.86[CEU][hapmap]
rs10456047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807008	1.00[CEU][hapmap]
rs10946820	0.86[CEU][hapmap]
rs10946821	0.86[CEU][hapmap]
rs10946823	0.92[CEU][hapmap]
rs10946824	0.86[CEU][hapmap]
rs10946825	0.91[CEU][hapmap]
rs10946826	0.86[CEU][hapmap]
rs10946827	0.85[CEU][hapmap]
rs10946829	0.86[CEU][hapmap]
rs10946832	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs10946842	1.00[JPT][hapmap]
rs1131936	0.93[CEU][hapmap]
rs11753257	1.00[YRI][hapmap]
rs11760103	1.00[YRI][hapmap]
rs12191917	0.86[CEU][hapmap]
rs12193283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194001	0.83[CEU][hapmap]
rs12194036	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12194073	0.86[CEU][hapmap]
rs12196371	1.00[CEU][hapmap]
rs12197304	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198993	0.86[CEU][hapmap]
rs12201546	0.86[CEU][hapmap]
rs12205310	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12206812	0.86[CEU][hapmap]
rs12207930	0.86[CEU][hapmap]
rs12208211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12208272	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][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]
rs12208788	0.93[CEU][hapmap]
rs12211872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12214444	1.00[CEU][hapmap]
rs12214486	0.86[CEU][hapmap]
rs12214924	0.86[CEU][hapmap]
rs12661560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12664899	0.93[CEU][hapmap]
rs17537465	0.93[CEU][hapmap]
rs17539219	0.86[CEU][hapmap]
rs17610161	1.00[CEU][hapmap]
rs17611220	0.86[CEU][hapmap]
rs17611438	0.85[CEU][hapmap]
rs1884945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393652	0.86[CEU][hapmap]
rs2393664	0.81[CEU][hapmap]
rs2893844	0.85[CEU][hapmap]
rs2893845	0.86[CEU][hapmap]
rs2893847	0.86[CEU][hapmap]
rs2893848	0.86[CEU][hapmap]
rs2893849	0.93[CEU][hapmap]
rs2893856	0.93[CEU][hapmap]
rs2893857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3198487	0.85[CEU][hapmap]
rs3208734	0.85[CEU][hapmap]
rs3757143	1.00[YRI][hapmap]
rs3846843	0.86[CEU][hapmap]
rs3846844	0.86[CEU][hapmap]
rs3846847	0.86[CEU][hapmap]
rs3846848	0.86[CEU][hapmap]
rs3846849	0.86[CEU][hapmap]
rs3902051	0.93[CEU][hapmap]
rs4083469	0.86[CEU][hapmap]
rs4609015	0.86[CEU][hapmap]
rs4711108	1.00[CEU][hapmap]
rs4711109	0.86[CEU][hapmap]
rs4711110	1.00[CEU][hapmap]
rs4711111	0.86[CEU][hapmap]
rs4712986	0.93[CEU][hapmap]
rs4712988	0.93[CEU][hapmap]
rs4712990	1.00[CEU][hapmap]
rs4712993	0.86[CEU][hapmap]
rs4712994	0.86[CEU][hapmap]
rs4712996	0.86[CEU][hapmap]
rs4712999	0.92[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4713000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713011	1.00[JPT][hapmap]
rs56034653	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6456722	0.85[CEU][hapmap]
rs6456724	0.93[CEU][hapmap]
rs6900725	0.86[CEU][hapmap]
rs6901245	0.84[CEU][hapmap]
rs6907302	0.86[AMR][1000 genomes]
rs6910023	0.86[CEU][hapmap]
rs6912934	0.93[CEU][hapmap]
rs6920986	0.86[CEU][hapmap]
rs6926878	0.86[CEU][hapmap]
rs6928454	0.86[CEU][hapmap]
rs6929846	0.86[CEU][hapmap]
rs72843766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355	0.93[CEU][hapmap]
rs7356849	0.93[CEU][hapmap]
rs7744254	0.86[CEU][hapmap]
rs7745238	0.86[CEU][hapmap]
rs7745767	0.86[CEU][hapmap]
rs7751280	0.86[CEU][hapmap]
rs7768108	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs7770214	0.86[CEU][hapmap]
rs882010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9295690	0.81[CEU][hapmap]
rs9467759	0.93[CEU][hapmap]

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	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	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
5	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
6	nsv1031938	chr6:26467182-26501897	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10484441	BTN2A2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26469600-26476600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:26471800-26474800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:26471800-26474800	Weak transcription	Small Intestine	intestine
4	chr6:26471800-26475000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:26471800-26475400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:26471800-26476400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:26471800-26478000	Weak transcription	Lung	lung
8	chr6:26473200-26475200	Weak transcription	Spleen	Spleen
9	chr6:26473400-26474800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:26473400-26475000	Active TSS	Stomach Smooth Muscle	stomach
11	chr6:26473600-26474800	Active TSS	Primary T cells fromperipheralblood	blood
12	chr6:26473600-26474800	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr6:26473600-26474800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:26473600-26474800	Active TSS	Brain Hippocampus Middle	brain
15	chr6:26473600-26474800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr6:26473600-26474800	Active TSS	Fetal Lung	lung
17	chr6:26473600-26474800	Active TSS	Fetal Muscle Leg	muscle
18	chr6:26473600-26474800	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr6:26473600-26474800	Active TSS	NHDF-Ad	bronchial
20	chr6:26473600-26474800	Active TSS	Osteobl	bone
21	chr6:26473600-26475000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:26473600-26475000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:26473600-26475200	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr6:26473600-26475200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:26473600-26475400	Active TSS	A549	lung
26	chr6:26473600-26475400	Active TSS	HSMMtube	muscle
27	chr6:26473600-26476400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:26473800-26474800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:26473800-26474800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:26473800-26474800	Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr6:26473800-26474800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:26473800-26474800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:26473800-26474800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:26473800-26474800	Active TSS	Brain Germinal Matrix	brain
35	chr6:26473800-26474800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:26473800-26474800	Active TSS	Brain Substantia Nigra	brain
37	chr6:26473800-26474800	Active TSS	Colon Smooth Muscle	Colon
38	chr6:26473800-26474800	Active TSS	Duodenum Mucosa	Duodenum
39	chr6:26473800-26474800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr6:26473800-26474800	Active TSS	Fetal Intestine Large	intestine
41	chr6:26473800-26474800	Active TSS	Fetal Kidney	kidney
42	chr6:26473800-26474800	Active TSS	Placenta	Placenta
43	chr6:26473800-26474800	Active TSS	Fetal Stomach	stomach
44	chr6:26473800-26474800	Active TSS	Ovary	ovary
45	chr6:26473800-26474800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr6:26473800-26474800	Active TSS	Rectal Smooth Muscle	rectum
47	chr6:26473800-26474800	Active TSS	Stomach Mucosa	stomach
48	chr6:26473800-26474800	Active TSS	Thymus	Thymus
49	chr6:26473800-26474800	Active TSS	NHLF	lung
50	chr6:26473800-26475000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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