Variant report

Variant	rs6778970
Chromosome Location	chr3:23935839-23935840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23934601..23938770-chr3:23957665..23961115,6	MCF-7	breast:
2	chr3:23927429..23929219-chr3:23934294..23936839,2	K562	blood:
3	chr3:23930243..23932089-chr3:23933446..23935951,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1133926	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs1135452	0.88[ASN][1000 genomes]
rs1136155	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11710679	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11711380	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11713246	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs11718625	1.00[GIH][hapmap];0.82[JPT][hapmap]
rs11922577	1.00[MEX][hapmap]
rs11922609	0.81[CHD][hapmap]
rs12497944	0.82[JPT][hapmap]
rs13314607	0.84[EUR][1000 genomes]
rs13318927	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13325754	0.92[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap]
rs17787211	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2001209	0.81[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs28623591	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34476593	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4131864	0.82[JPT][hapmap];0.93[MEX][hapmap]
rs4619736	0.84[ASN][1000 genomes]
rs5001573	0.88[ASN][1000 genomes]
rs61645368	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6550809	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6773828	0.88[ASN][1000 genomes]
rs6787216	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6789983	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6800407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72627066	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73825116	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73825124	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73825170	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73825178	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73825181	0.90[EUR][1000 genomes]
rs7629325	0.88[EUR][1000 genomes]
rs7633520	0.93[ASN][1000 genomes]
rs7637968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8933	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9755750	0.93[ASN][1000 genomes]
rs9815334	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9834166	0.88[EUR][1000 genomes]
rs9836860	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9836970	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9850255	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9856727	0.84[EUR][1000 genomes]
rs9857442	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9862416	0.88[ASN][1000 genomes]
rs9863674	0.81[EUR][1000 genomes]
rs9875213	0.81[EUR][1000 genomes]
rs9876561	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6778970	ZNF385D	cis	parietal	SCAN
rs6778970	NKIRAS1	cis	parietal	SCAN
rs6778970	NR1D2	cis	Temporal Cortex	GTEx
rs6778970	NKIRAS1	cis	cerebellum	SCAN
rs6778970	NKIRAS1	Cis_1M	lymphoblastoid	RTeQTL
rs6778970	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23901200-23942000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:23907600-23940200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:23908000-23940200	Weak transcription	Gastric	stomach
4	chr3:23916000-23950200	Weak transcription	Aorta	Aorta
5	chr3:23916200-23948800	Weak transcription	Colonic Mucosa	Colon
6	chr3:23919000-23940000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:23919200-23938400	Weak transcription	Ovary	ovary
8	chr3:23919200-23940200	Weak transcription	Pancreas	Pancrea
9	chr3:23920000-23939000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:23920800-23940200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:23922400-23956600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:23922600-23936000	Weak transcription	Right Ventricle	heart
13	chr3:23922600-23940000	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:23923000-23956600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:23923400-23955200	Weak transcription	Thymus	Thymus
16	chr3:23923400-23957000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:23923600-23956800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:23924000-23939000	Weak transcription	Fetal Brain Male	brain
19	chr3:23924200-23957800	Weak transcription	Esophagus	oesophagus
20	chr3:23924200-23957800	Weak transcription	Lung	lung
21	chr3:23924400-23940200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:23924600-23936000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:23924600-23940000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:23924600-23940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:23925000-23936000	Weak transcription	Spleen	Spleen
26	chr3:23925000-23940200	Weak transcription	Fetal Brain Female	brain
27	chr3:23925800-23937200	Strong transcription	GM12878-XiMat	blood
28	chr3:23928000-23957200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:23928200-23939800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:23928800-23956000	Weak transcription	Small Intestine	intestine
31	chr3:23928800-23957400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr3:23929000-23937400	Strong transcription	Fetal Intestine Large	intestine
33	chr3:23929000-23956600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:23929400-23937200	Strong transcription	Dnd41	blood
35	chr3:23929800-23944200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:23930000-23936000	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr3:23930200-23936000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:23930600-23945800	Weak transcription	Fetal Heart	heart
39	chr3:23930800-23937600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:23930800-23954800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:23930800-23956800	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:23931000-23936600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:23931000-23936600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:23931200-23937400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:23931200-23945800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:23931600-23936200	Strong transcription	A549	lung
47	chr3:23931600-23936200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:23931600-23937000	Strong transcription	Liver	Liver
49	chr3:23931600-23937200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr3:23931600-23942600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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