Variant report

Variant	rs9875616
Chromosome Location	chr3:45979877-45979878
allele	A/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	CTCF	chr3:45979760-45979910	AG10803	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:45978760..45981889-chr3:46119716..46121321,25	MCF-7	breast:
2	chr3:45978904..45980774-chr3:45983050..45984937,2	MCF-7	breast:
3	chr3:45979673..45982315-chr3:46020948..46022553,2	K562	blood:

Variant related genes	Relation type
CXCR6	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11130078	0.96[ASN][1000 genomes]
rs13064616	0.81[ASN][1000 genomes]
rs1388605	0.83[CEU][hapmap]
rs1392288	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1463680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500003	0.88[ASN][1000 genomes]
rs1546076	0.83[CEU][hapmap]
rs1809733	0.83[CEU][hapmap]
rs1846615	0.88[ASN][1000 genomes]
rs1873001	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]
rs2129879	0.81[ASN][1000 genomes]
rs2129881	0.81[ASN][1000 genomes]
rs2133660	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]
rs2171528	0.81[ASN][1000 genomes]
rs2171529	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs2234350	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276855	0.85[ASN][1000 genomes]
rs2276856	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2373155	0.91[CEU][hapmap]
rs3796374	0.88[ASN][1000 genomes]
rs3947589	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs4682801	0.83[CEU][hapmap]
rs4683158	0.83[CEU][hapmap]
rs4683165	0.81[ASN][1000 genomes]
rs55844314	0.88[ASN][1000 genomes]
rs57651127	0.85[ASN][1000 genomes]
rs57837898	0.85[ASN][1000 genomes]
rs6786959	0.80[CEU][hapmap]
rs6802312	0.83[CEU][hapmap]
rs751667	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs7612402	0.81[ASN][1000 genomes]
rs7653682	0.83[CEU][hapmap]
rs9820016	0.83[CEU][hapmap]
rs9844821	0.88[ASN][1000 genomes]
rs9869848	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer 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	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9875616	CXCR6	cis	parietal	SCAN
rs9875616	ARIH2	cis	cerebellum	SCAN
rs9875616	RNF123	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:45958800-45980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:45958800-45980200	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
5	chr3:45959200-45980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:45959800-45980400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:45960000-45980400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:45960400-45980200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:45963200-45985200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:45964400-45980400	Weak transcription	Fetal Brain Female	brain
12	chr3:45965400-45980400	Weak transcription	Fetal Brain Male	brain
13	chr3:45966000-45980600	Weak transcription	HMEC	breast
14	chr3:45967200-45980000	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:45968600-45980200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr3:45970000-45980400	Weak transcription	Right Atrium	heart
17	chr3:45970200-45980400	Weak transcription	NH-A	brain
18	chr3:45970200-45980600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:45970200-45988200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:45971000-45980200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr3:45971400-45980200	Strong transcription	Dnd41	blood
22	chr3:45971800-45982400	Weak transcription	NHEK	skin
23	chr3:45972800-45988600	Weak transcription	Small Intestine	intestine
24	chr3:45973400-45986400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:45973600-45980600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:45973800-45988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:45973800-45991400	Weak transcription	Brain Germinal Matrix	brain
28	chr3:45974000-45980600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:45974400-45988000	Weak transcription	Fetal Kidney	kidney
30	chr3:45974600-45980000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:45975400-45980600	Weak transcription	NHDF-Ad	bronchial
32	chr3:45976400-45980000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:45976400-45980600	Strong transcription	Fetal Intestine Small	intestine
34	chr3:45976400-45981800	Strong transcription	Fetal Stomach	stomach
35	chr3:45976800-45980600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:45977000-45980600	Weak transcription	Psoas Muscle	Psoas
37	chr3:45977200-45980200	Strong transcription	Left Ventricle	heart
38	chr3:45977200-45980600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:45977400-45980400	Weak transcription	Fetal Heart	heart
40	chr3:45977400-45987000	Weak transcription	Fetal Lung	lung
41	chr3:45977400-45988000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:45977600-45983400	Weak transcription	Primary B cells from cord blood	blood
43	chr3:45977600-45987600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:45978000-45988000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:45978200-45980200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:45978200-45980400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:45978200-45980400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:45978200-45980400	Weak transcription	GM12878-XiMat	blood
49	chr3:45978200-45982200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:45978200-45988200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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