Variant report

Variant	rs6946418
Chromosome Location	chr7:129297916-129297917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10215964	0.89[YRI][hapmap]
rs10236959	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10270813	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10275592	0.88[YRI][hapmap]
rs10808240	0.87[YRI][hapmap]
rs12666331	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1562833	0.89[YRI][hapmap]
rs1882094	0.93[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];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962039	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs2001583	0.81[AMR][1000 genomes]
rs2402966	0.94[YRI][hapmap]
rs2402968	1.00[YRI][hapmap]
rs3778775	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4272311	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4728174	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs62489295	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6467257	0.94[YRI][hapmap]
rs6957596	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6958375	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6967348	0.89[YRI][hapmap]
rs6969441	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7778085	0.94[YRI][hapmap]
rs7778681	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7781972	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7782520	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9641854	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9656383	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9792084	0.83[YRI][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6946418	TNFRSF8	trans	cerebellum	SCAN
rs6946418	TNPO3	cis	parietal	SCAN
rs6946418	TNPO3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129283800-129331600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:129284600-129298200	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:129286600-129299400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:129286600-129301600	Weak transcription	HSMMtube	muscle
5	chr7:129286800-129304400	Weak transcription	NHLF	lung
6	chr7:129287000-129298200	Weak transcription	Fetal Heart	heart
7	chr7:129287200-129301600	Weak transcription	Psoas Muscle	Psoas
8	chr7:129287800-129299600	Weak transcription	NH-A	brain
9	chr7:129289200-129314000	Weak transcription	Fetal Brain Male	brain
10	chr7:129290000-129299600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:129290000-129325800	Weak transcription	Stomach Mucosa	stomach
12	chr7:129290400-129304600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr7:129290600-129299400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:129293600-129301600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:129293800-129311200	Weak transcription	Brain Anterior Caudate	brain
16	chr7:129293800-129311400	Weak transcription	Brain Angular Gyrus	brain
17	chr7:129294000-129300400	Weak transcription	Fetal Brain Female	brain
18	chr7:129296000-129298200	Weak transcription	Colonic Mucosa	Colon
19	chr7:129296600-129299600	Strong transcription	Fetal Thymus	thymus
20	chr7:129296600-129301600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:129296800-129298000	Enhancers	HMEC	breast
22	chr7:129296800-129298000	Genic enhancers	NHEK	skin
23	chr7:129296800-129298200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:129296800-129298200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:129296800-129299000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr7:129296800-129299400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:129296800-129299400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr7:129296800-129300600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr7:129296800-129300600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr7:129296800-129301400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:129297000-129298000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:129297000-129298400	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr7:129297000-129298400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:129297000-129298600	Strong transcription	Thymus	Thymus
35	chr7:129297000-129298800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:129297000-129299200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:129297000-129299200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr7:129297000-129299200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:129297000-129299400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr7:129297000-129299400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr7:129297000-129299400	Strong transcription	GM12878-XiMat	blood
42	chr7:129297000-129299600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr7:129297000-129299600	Strong transcription	K562	blood
44	chr7:129297000-129300200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:129297000-129300200	Strong transcription	Primary T cells from cord blood	blood
46	chr7:129297000-129300200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr7:129297000-129300400	Strong transcription	Primary B cells from cord blood	blood
48	chr7:129297000-129300400	Strong transcription	Fetal Intestine Large	intestine
49	chr7:129297000-129300400	Strong transcription	Placenta	Placenta
50	chr7:129297000-129300600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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