Variant report

Variant	rs240768
Chromosome Location	chr6:100957344-100957345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:100940983..100941708-chr6:100956888..100957470,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12661493	0.94[ASN][1000 genomes]
rs12662153	0.94[ASN][1000 genomes]
rs12663913	0.91[ASN][1000 genomes]
rs1501356	0.94[ASN][1000 genomes]
rs17060762	0.88[ASN][1000 genomes]
rs171257	0.83[EUR][1000 genomes]
rs2398133	0.97[EUR][1000 genomes]
rs240165	0.87[EUR][1000 genomes]
rs240166	0.90[EUR][1000 genomes]
rs240777	0.97[EUR][1000 genomes]
rs240779	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs240782	0.97[EUR][1000 genomes]
rs240785	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs3213542	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33988845	0.97[EUR][1000 genomes]
rs401864	0.80[CEU][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap]
rs6931919	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72939355	0.97[EUR][1000 genomes]
rs72949504	0.97[EUR][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	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Economic and political preferences (immigration/crime)	22566634	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs240768	GRIK2	cis	Artery Tibial	GTEx
rs240768	CCNC	cis	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100949800-100966400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:100950200-100959000	Weak transcription	Pancreas	Pancrea
3	chr6:100950400-100959200	Weak transcription	Gastric	stomach
4	chr6:100951200-100959200	Weak transcription	Left Ventricle	heart
5	chr6:100951400-100959400	Weak transcription	HepG2	liver
6	chr6:100951400-100960000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:100951600-100969800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:100952400-100959800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:100952600-100967600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:100952800-100959000	Weak transcription	Fetal Intestine Small	intestine
11	chr6:100952800-100997400	Weak transcription	A549	lung
12	chr6:100953000-100959000	Weak transcription	Fetal Stomach	stomach
13	chr6:100953000-100959200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:100953000-100968400	Weak transcription	Fetal Kidney	kidney
15	chr6:100953200-100959400	Weak transcription	NHEK	skin
16	chr6:100953200-100959600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:100953200-100960000	Weak transcription	GM12878-XiMat	blood
18	chr6:100953200-100966200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:100953400-100959000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:100953400-100959000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:100953400-100966600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:100953400-100967400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:100953600-100960200	Weak transcription	Aorta	Aorta
24	chr6:100953600-100960400	Weak transcription	NHLF	lung
25	chr6:100953800-100958400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:100954000-100959200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:100954000-100959200	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:100954200-100959200	Weak transcription	Lung	lung
29	chr6:100954200-100959800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:100954200-100960800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:100954200-100961000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:100954200-100966200	Strong transcription	Dnd41	blood
33	chr6:100954600-100986200	Weak transcription	Spleen	Spleen
34	chr6:100954800-100957600	Strong transcription	HMEC	breast
35	chr6:100954800-100960600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:100954800-100966200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:100955000-100959200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr6:100955000-100959600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:100955000-100959800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:100955000-100960000	Weak transcription	HSMMtube	muscle
41	chr6:100955000-100960000	Weak transcription	NH-A	brain
42	chr6:100955000-100960200	Weak transcription	Stomach Mucosa	stomach
43	chr6:100955000-100962800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:100955200-100959200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:100955200-100960000	Weak transcription	Fetal Thymus	thymus
46	chr6:100955200-100960200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:100955200-100961000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr6:100955200-100962200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:100955200-100972800	Weak transcription	Right Ventricle	heart
50	chr6:100955400-100958600	Strong transcription	HSMM	muscle

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